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

• is participating in this redox process is surrounded by extended aromatic rings bearing 1,3-dithiol rings. Conclusion We have synthesized novel multistage TTF derivatives 1–4 bearing 6-aryl-1,4-dithiafulvene moieties by palladium-catalyzed direct C–H arylation. The DFT calculations revealed the

Cation-induced ring-opening and oxidation reaction of photoreluctant spirooxazine–quinolizinium conjugates

• Phil M. Pithan,
• Sören Steup and
• Heiko Ihmels

Beilstein J. Org. Chem. 2020, 16, 904–916, doi:10.3762/bjoc.16.82

• discussed in the literature whether metal cations are coordinated in a monodentate fashion to the phenolate oxygen atom or rather in a bidentate fashion both to the phenolate oxygen and the imine nitrogen atoms of the open merocyanine form [25][28]. Furthermore, density functional theory (DFT) calculations

Bipyrrole boomerangs via Pd-mediated tandem cyclization–oxygenation. Controlling reaction selectivity and electronic properties

• Liliia Moshniaha,
• Marika Żyła-Karwowska,
• Joanna Cybińska,
• Piotr J. Chmielewski,
• Ludovic Favereau and
• Marcin Stępień

Beilstein J. Org. Chem. 2020, 16, 895–903, doi:10.3762/bjoc.16.81

• using NMR spectroscopy and DFT calculations [33]. In particular, the unprecedented double α-oxygenation of bipyrroles was shown to occur through stepwise acetoxylation, which we found to compete with α–α oligomerization. These new bipyrrole boomerangs exhibited enhanced fluorescence with Φfl values of

• DFT calculations (Figure 1 and Supporting Information File 1). The length of the linker (n) in cNDAnX and cNMInX controls the in- and out-of-plane geometry of the chromophore. The observed changes can be expressed in terms of two parameters: α, the angle between the monopyrrole axis and the N–N vector

• measurements, without any significant loss of the unpolarized emission intensity. This behavior, which precluded a quantitative analysis of the CPL properties, may be attributed to a photoinduced racemization process. The differences in configurational stability of boomerangs are reproduced by DFT calculations

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

• -membered rings on the peropyrene core, the electronic structures and the frontier orbitals of the peropyrene derivative 6 without pentagons and of compound 1 are compared by DFT calculations at the B3LYP/6-311++G(d,p) level. As shown in Figure 4, the LUMO and HOMO of 6 are both delocalized over the

• -diphenylpyrene is the key step. The single crystal X-ray diffraction analysis revealed a twisted structure of 1 due to the steric hindrance at the bay positions. From the bond length analysis and DFT calculations, CP-PAH 1 consists of the aromatic peropyrene core with two slightly antiaromatic peri-fused five

Recent advances in Cu-catalyzed C(sp³)–Si and C(sp³)–B bond formation

• Balaram S. Takale,
• Ruchita R. Thakore,
• Elham Etemadi-Davan and
• Bruce H. Lipshutz

Beilstein J. Org. Chem. 2020, 16, 691–737, doi:10.3762/bjoc.16.67

• an appropriate electrophile led to C–C bond formation, ultimately delivering chiral tertiary alcohols. Mechanistic studies and DFT calculations showed that an in situ-formed borylcopper(I) species is responsible for the 1,2-addition (Scheme 73) [136]. C,O-Diboration of ketones 464 was explored using

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

• fluorescence at 576 nm with a quantum yield of ΦF = 0.86 at 298 K (Figure 3). Both peaks are slightly red-shifted relative to those of intact terrylene (λabs = 560 nm and λem = 571 nm with ΦF = 0.82 in toluene). We employed density functional theory (DFT) and time-dependent (TD)-DFT calculations, both of them

• distributions is negligible because of the existence of node at 2,5,10,13-positions. The longest band of TB4 at 563 nm comprises the transition from equally destabilized HOMO (−4.29 eV) to LUMO (−1.99 eV) (oscillator strength, f = 0.86). The transition energies and oscillator strengths simulated by TD-DFT

• calculations showed a good agreement with the observed absorption spectra. Taking the successful result of the terrylene borylation, next we tried to perform the same reaction to quaterrylene (Scheme 2). The quaterrylene was prepared by the oxidative condensation reaction of perylene with TfOH and DDQ [9

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

• , density functional theory (DFT) calculations were performed at the B3LYP/6-31G(d) level of theory. The a2-symmetry of the HOMOs and b2-symmetry of the LUMOs of each, the α- and β-ethynyl-substituted BODIPYs are almost identical to those of the unsubstituted compound 1a (Figure S24, Supporting Information

• , and DFT calculations. Supporting Information File 167: Crystallographic information file of compound 3a. Supporting Information File 168: Crystallographic information file of compound 6b. Acknowledgements We thank Dr. T. Ono at Kyushu University for the help of absolute photoluminescence quantum

Six-fold C–H borylation of hexa-peri-hexabenzocoronene

• Mai Nagase,
• Kenta Kato,
• Akiko Yagi,
• Yasutomo Segawa and
• Kenichiro Itami

Beilstein J. Org. Chem. 2020, 16, 391–397, doi:10.3762/bjoc.16.37

• hexaborylated HBC 1. The structure of thus-obtained 1 was confirmed by X-ray crystallography, and the electronic effects of the boryl groups were investigated through optoelectronic measurements and density functional theory (DFT) calculations. Results and Discussion We have examined the conditions for C–H

• from the singlet excited state were determined (kr = 2.0 × 106 s−1; knr = 7.9 × 107 s−1). The frontier molecular orbitals of 1 calculated by DFT calculations at the B3LYP/6-31G(d) level of theory are shown in Figure 4b. Owing to the highly symmetrical structure of 1, both its HOMO and HOMO−1 as well as

• present method. The analyzed structure from X-ray crystallography confirmed the regioselective C–H borylations at the least sterically hindered C–H bonds of HBC. Optoelectronic measurements of 1 revealed bathochromic shifts of the absorption bands compared with unsubstituted HBC. DFT calculations also

Copper-catalyzed enantioselective conjugate addition of organometallic reagents to challenging Michael acceptors

• Delphine Pichon,
• Jennifer Morvan,
• Christophe Crévisy and
• Marc Mauduit

Beilstein J. Org. Chem. 2020, 16, 212–232, doi:10.3762/bjoc.16.24

• in moderate to good yields (28–85%) with remarkable regio- (>95%) and enantioselectivities (91–95% ee) [39]. Interestingly, DFT calculations supported the crucial role of the imidazole moiety towards the 1,4-addition (vs 1,6 or 1,8) [39]. Thanks to the efficient post-transformation of the

Synthesis of 4-(2-fluorophenyl)-7-methoxycoumarin: experimental and computational evidence for intramolecular and intermolecular C–F···H–C bonds

• Vuyisa Mzozoyana,
• Fanie R. van Heerden and
• Craig Grimmer

Beilstein J. Org. Chem. 2020, 16, 190–199, doi:10.3762/bjoc.16.22

• crystal structure and solution-state NMR data of the coumarin 6 were studied to examine any C–F···H–C hydrogen bond interactions. DFT calculations were performed to determine the preferred conformations of the structure that might exhibit a C–F···H–C hydrogen bond. Results and Discussion Synthesis of 2

[1,3]/[1,4]-Sulfur atom migration in β-hydroxyalkylphosphine sulfides

• Katarzyna Włodarczyk,
• Piotr Borowski and
• Marek Stankevič

Beilstein J. Org. Chem. 2020, 16, 88–105, doi:10.3762/bjoc.16.11

• control experiments and DFT calculations. Keywords: Brønsted and Lewis acids; DFT; mechanistic studies; rearrangement; stereochemistry; sulfur atom migration; Introduction Among all organic reactions, rearrangements are an exciting class of transformations where unusual or even unexpected products can

• dissociation are ca. 34.6 kcal/mol for the secondary alcohol 8, ca. 23.3 kcal/mol for the mesylate 60, and ca. 25.0 kcal/mol for the tertiary alcohol 20, as estimated by DFT calculations. The value for mesylate roughly fitted the range according to which the reaction may proceed at room temperature. For

• activation by AlCl3 impossible, which prevented the rearrangement. To gain detailed insights into the possible reaction mechanism, DFT calculations were performed on model β-hydroxyalkylphosphine sulfide 20, possessing two ethyl groups at the β-carbon atom. First, the Brønsted acid-catalyzed rearrangement

Halogen-bonding-induced diverse aggregation of 4,5-diiodo-1,2,3-triazolium salts with different anions

• Xingyu Xu,
• Shiqing Huang,
• Zengyu Zhang,
• Lei Cao and
• Xiaoyu Yan

Beilstein J. Org. Chem. 2020, 16, 78–87, doi:10.3762/bjoc.16.10

• understand the 1,2,3-triazole based XB donors, model 1,2,3-triazole A, 1,2,3-triazolium B, 1,2,3-triazolylidene complex C-CuI and diiodotriazolium D were calculated by DFT calculations (Figure 9). The calculation results show that σ holes in diiodotriazolium D are mainly located in the elongation of two C–I

Synthesis and characterization of bis(4-amino-2-bromo-6-methoxy)azobenzene derivatives

• David Martínez-López,
• Amirhossein Babalhavaeji,
• Diego Sampedro and
• G. Andrew Woolley

Beilstein J. Org. Chem. 2019, 15, 3000–3008, doi:10.3762/bjoc.15.296

• of intramolecular H-bond formation, we wished to retain at least one methoxy group. To reduce the rate of thermal reversion, only derivatives with substituents in all four ortho-positions were considered. Time-dependent density functional theory (TD-DFT) calculations were used to predict the

• periodically scanned (250 to 600 nm for each scan; integration time: 2s; scan speed: 480 nm/min) in 2-minute intervals. Absorbance data vs time were then fitted to a single exponential equation to obtain thermal relaxation half-lives using Equation 1. Computational methods DFT calculations were performed using

• out TD-DFT calculations for conformer 2. Second, for the neutral species, the N=N–C–C dihedral angles in the optimized structures were manually set to 20° to generate new input files. Reoptimization yielded the same structures and free energies. The optimized geometries of all structures were

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. Furthermore, these organocatalysts slowed down the Ireland–Claisen rearrangement in comparison to an uncatalyzed reaction. The catalyst-free reaction proceeded well in green solvents or without any solvent. DFT calculations showed that the activation barriers are higher for reactions involving

• hydrogen-donating organocatalysts and kinetic experiments suggest that the catalysts bind stronger to the starting silyl ketene acetals than to transition structures thus leading to inefficient rearrangement reactions. Keywords: DFT calculations; green solvents; H-bonding catalysts; Ireland–Claisen

• Chiral hydrogen-bond-donating organocatalysts such as thioureas, squaramides, or alcohols failed to catalyze the Ireland–Claisen rearrangement of silyl ketene acetals. Comparison experiments showed that increasing catalyst loading gradually slowed-down the reaction. DFT calculations using long-range

Synthesis and optoelectronic properties of benzoquinone-based donor–acceptor compounds

• Daniel R. Sutherland,
• Nidhi Sharma,
• Georgina M. Rosair,
• Ifor D. W. Samuel,
• Ai-Lan Lee and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2019, 15, 2914–2921, doi:10.3762/bjoc.15.285

• carbazoles with respect to the bridging benzene of ca. 44° in both 3 and 4 (Figure 2). Theoretical properties Density functional theory (DFT) calculations were performed in the gas phase to assess the electronic structures of 2–5 (see Supporting Information File 1 for details). The S1 and T1 excited states

• ) and differential pulse voltammograms (DPVs) are shown in Figure 4 and the data are summarized in Table 1. Upon scanning to negative voltage, all four compounds exhibited two highly reversible reduction waves, a typical behavior of the BQ moiety in aprotic solvents [32]. Based on DFT calculations and a

A chiral self-sorting photoresponsive coordination cage based on overcrowded alkenes

• Constantin Stuckhardt,
• Diederik Roke,
• Wojciech Danowski,
• Edwin Otten,
• Sander J. Wezenberg and
• Ben L. Feringa

Beilstein J. Org. Chem. 2019, 15, 2767–2773, doi:10.3762/bjoc.15.268

• supramolecular coordination complexes consisting of a Pd2L4 stoichiometry. As shown by NMR, CD and X-ray studies, as well as DFT calculations, these complexes form cage-like structures by chiral self-sorting. Photochromic ligands derived from first generation molecular motors enable light-driven interconversion

• enantiomeric cages in which the Pd–Pd axis of each cage is located at the 4-fold rotation axis. This means that the cage structure is made up with exclusively (R,R) or (S,S) enantiomer of the ligand and that the elementary cell is built from the racemic pair of cages. DFT calculations were performed to gain

• different cage structures. Interestingly, the cage structures with Pd2L4 constitution were shown to be homochiral, forming single diastereomers as evident from NMR, CD and X-ray analysis, supported by DFT calculations. Additionally, the cage structures were able to bind OTs− inside their cavity. Although

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

• photoswitching. Table 2 summarizes the theoretical excitation energy separation (in nm) between the characteristic n–π* and π–π* transitions in the ortho-substituted arylazopyrazoles under study. Theoretical TD-DFT calculations indicate that the family of ortho-substituted 4pzH-X presents well-separated n–π

• directly impacts the Z–E photoconversion efficiency, and thus lower PSSs of 77, 85 and 73% are recorded for 4pzMe-F2, 4pzMe-Cl2 and 4pzMe-OMe2, respectively, versus >98% for 4pzMe. Similarly, 4pzH-F2 possesses a lower PSS versus 4pzH (42% versus 70%). While inaccuracies in the DFT calculations may explain

Emission solvatochromic, solid-state and aggregation-induced emissive α-pyrones and emission-tuneable 1H-pyridines by Michael addition–cyclocondensation sequences

• Natascha Breuer,
• Irina Gruber,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2019, 15, 2684–2703, doi:10.3762/bjoc.15.262

• emission solvatochromism. Also a donor-substituted α-pyrone shows pronounced aggregation-induced emission enhancement. Keywords: cyclocondensation; DFT calculations; fluorescence; heterocycles; 1H-pyridines; α-pyrones; Introduction A high sensitivity and precise tuneability of fluorescence colors are

• photophysical studies (absorption and emission spectroscopy) and the studies on the electronic structure were accompanied by TD-DFT calculations for assigning the dominant longest-wavelength absorption bands. Results and Discussion Synthesis and tentative mechanism Recently, we reported a straightforward access

• ). The Onsager radius a, assuming a spherical dipole to approximate the molecular volume of the molecule in solution, was estimated from the optimized ground-state structure of compound 6c obtained by DFT calculations. With an a value of 5.46 Å, the change in dipole moment was calculated to 11.6 D (3.87

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

• -soluble and selective bioprobe for plasma membrane imaging. The new compound was efficiently synthesized in a two-step procedure with good yields. The photophysical properties were evaluated and the dye proved to have an excellent photostability in several solvents. DFT calculations were found in

• density functional theory (TD-DFT). In practice, when applying DFT calculations, there is no “universal” exchange correlation functional (XCF), thus the performance of different XCFs in simulating the absorption spectra of BTD-4APTEG had to be assessed. We aimed at describing the maxima absorption peak

• agreed well with the experimental data obtained for the newly developed dye. DFT calculations were also employed to forecast the lipophilic character of the dye utilizing several XCFs. Experimentally, lipophilicity can be measured by means of the logarithm of the n-octanol/water partition coefficient

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

• and studied by multiple gas-phase techniques, ESI-QTOF-MS, IRMPD, and DT-IMMS experiments, as well as DFT calculations. The comparison of classical resorcinarenes with pyridinearenes by MS and NMR experiments reveals clear differences in their host–guest chemistry and implies that cation encapsulation

• in pyridine[4]arene is an anion-driven process. Keywords: cation binding; DFT calculations; ion mobility mass spectrometry; macrocycles; pyridinearenes; resorcinarenes; Introduction Resorcinarenes and their derivatives are known for the molecular recognition properties of their self-assembled

• could not be verified and the anions were assumed to interact with the pyridinearene cavity. Inclusion complexes of anions within pyridinearene dimers were also theoretically studied by DFT calculations, but using a truncated pyridinearene dimer model [8]. However, previous studies have also shown that

Photochromic diarylethene ligands featuring 2-(imidazol-2-yl)pyridine coordination site and their iron(II) complexes

• Andrey G. Lvov,
• Max Mörtel,
• Anton V. Yadykov,
• Frank W. Heinemann,
• Valerii Z. Shirinian and
• Marat M. Khusniyarov

Beilstein J. Org. Chem. 2019, 15, 2428–2437, doi:10.3762/bjoc.15.235

• good accordance with previous DFT calculations [37], the molecule shows exclusively antiparallel conformation [8] of the thiophene and imidazole groups of the photoactive diarylethene moiety, with the respective α-methyl groups pointing in different directions. The thiophene and imidazole rings are

Effect of ring size on photoisomerization properties of stiff stilbene macrocycles

• Sandra Olsson,
• Óscar Benito Pérez,
• Magnus Blom and
• Adolf Gogoll

Beilstein J. Org. Chem. 2019, 15, 2408–2418, doi:10.3762/bjoc.15.233

• a six carbon chain) showed some degree of isomerization when irradiated. DFT calculations of the energy differences between the E- and Z-isomers show the same trend as the experimental results. Interestingly the DFT study highlights that the energy difference between the E- and Z-isomers of even the

• been synthesised and used to investigate the effect of the ring size on the photoisomerization of the stiff stilbene unit. Both experimental photoisomerization and DFT calculations show that the strain of the linking chain affects the isomerization even for the longest chains. As stiff stilbene is

• Shimadzu UV-1650PC spectrophotometer using 10 mm quartz cuvettes. Photoisomerizations were performed using an Oriel 1000 W Xe ARC light source equipped with a band pass filter 10BPF10-300 or 10BPF10-280 (Newport). Computational details The DFT calculations on the stiff stilbene macrocycles were performed

Reversible switching of arylazopyrazole within a metal–organic cage

• Anton I. Hanopolskyi,
• Soumen De,
• Michał J. Białek,
• Yael Diskin-Posner,
• Liat Avram,
• Moran Feller and
• Rafal Klajn

Beilstein J. Org. Chem. 2019, 15, 2398–2407, doi:10.3762/bjoc.15.232

• switching to the Z isomer was accompanied by the release of one of the two guests from the cage and the formation of a 1:1 cage/Z-arylazopyrazole inclusion complex. DFT calculations suggest that this process involves a dramatic change in the conformation of the cage. Back-isomerization was induced with

• -ray diffraction. To obtain hints about the packing of Z-1 within 2, we therefore performed density functional theory (DFT) calculations. Compared with the complex before photoisomerization, the cage in (Z-1)2 is severely distorted (Figure 5; see also Supporting Information File 3), assuming a bowl

• 1:1 complexes of 2 with the Z isomers of various azobenzenes are notoriously difficult to crystallize [18]. We believe that the insights by DFT calculations reported here for (Z-1)2 can be extended to the complexes of 2 with other Z-azo guests as well. To gain further insight into the

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

• rearrangement. Hong and Tantillo performed the first theoretical study of the reaction mechanism in CotB2 via gas phase density functional theory (DFT) calculations [33]. Simultaneously, Sato et al. also studied the CotB2 reaction mechanism in the gas phase using DFT, combined with experimental deuterium

Synthesis of a dihalogenated pyridinyl silicon rhodamine for mitochondrial imaging by a halogen dance rearrangement

• Jessica Matthias,
• Thines Kanagasundaram,
• Klaus Kopka and
• Carsten S. Kramer

Beilstein J. Org. Chem. 2019, 15, 2333–2343, doi:10.3762/bjoc.15.226

• microscopy [2][3][4][5][6][7][8][9], as direct probes for various biomolecules [10][11][12][13] or as sensors for metal ions [14][15][16][17][18], pH [16], voltage [19] or metabolites [20][21][22][23]. Several attempts were made, partially supported by DFT calculations, to correlate the dyes’ structural

• experiments (supported by DFT calculations) on the orbital effects of both halogens and the nitrogen position in the pyridine ring are needed to explain these effects with confidence. In addition, our SiR dye 15 displays photophysical properties (extinction coefficient, quantum yield, lifetime) in the same