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

Small anion-assisted electrochemical potential splitting in a new series of bistriarylamine derivatives: organic mixed valency across a urea bridge and zwitterionization

• Keishiro Tahara,
• Tetsufumi Nakakita,
• Alyona A. Starikova,
• Takashi Ikeda,
• Masaaki Abe and
• Jun-ichi Kikuchi

Beilstein J. Org. Chem. 2019, 15, 2277–2286, doi:10.3762/bjoc.15.220

• for 1b. The larger splitting for 1b with respect to 1a is a common feature between DFT calculations and electrochemical investigations. This indicates that electronic interactions between the NAr3 units largely contribute to the experimentally proven thermodynamic stability of the MV state. Indeed

• of counteranion size, as discussed in the next section. Characterization of 1 in the MV state DFT calculations were performed to obtain theoretical information about the MV state. The planarity of the urea moiety and the phenyl groups on both sides remained almost unchanged upon one-electron

• binding strength to PF6−, suggesting an involvement of the 1+–PF6− species during the electrochemical event of 1 described above. The comparison of DFT calculations between 1+ and 1+–PF6− revealed that upon zwitterion formation, the bound PF6− can increase the electronic interactions between the NAr3

Click chemistry towards thermally reversible photochromic 4,5-bisthiazolyl-1,2,3-triazoles

• Chenxia Zhang,
• Kaori Morinaka,
• Mahmut Kose,
• Takashi Ubukata and
• Yasushi Yokoyama

Beilstein J. Org. Chem. 2019, 15, 2161–2169, doi:10.3762/bjoc.15.213

• Supporting Information File 1). The absorption spectral properties are summarized in Table 1 together with their predicted absorption maxima obtained by TD DFT calculations in vacuum [35]. Although 1o and 2o showed substantial coloration, 3o showed only a slight coloration at room temperature. The solvent

• observation was well-reproduced by TD DFT calculations (Table 1 and chapter SI-4 in Supporting Information File 1). When the absorption maximum wavelength of 1c, whose central ethene moiety is triazole, is compared with those of the closely related 7c (cyclopentene) [37], 8c (hexafluorocyclopentene) [38], 9c

• bond length nor its bond order, which were obtained by DFT calculations of these compounds, did not give a clear explanation for the difference in the reaction rate. Possible evidence of the fast back reaction of 3c may be found in the bond lengths and Mulliken bond orders between the atoms

Friedel–Crafts approach to the one-pot synthesis of methoxy-substituted thioxanthylium salts

• Kenta Tanaka,
• Yuta Tanaka,
• Mami Kishimoto,
• Yujiro Hoshino and
• Kiyoshi Honda

Beilstein J. Org. Chem. 2019, 15, 2105–2112, doi:10.3762/bjoc.15.208

• examined using MeCN, CH3NO2, DMSO and MeOH, no substantial shifts of the main peak at around 460 nm in the UV–vis absorption spectra were observed [24], indicating that the main absorption of these catalysts would be due to π–π* transition, which is supported by DFT calculations (TD-DFT B3LYP method

• electron-withdrawing groups can be applied to the reaction. It was found that the main absorption of thioxanthylium salts around 460 nm in UV–vis spectra would be due to π–π* transitions, which was supported by DFT calculations. The present reaction provides a versatile access to functionalized

α-Photooxygenation of chiral aldehydes with singlet oxygen

• Dominika J. Walaszek,
• Magdalena Jawiczuk,
• Jakub Durka,
• Olga Drapała and
• Dorota Gryko

Beilstein J. Org. Chem. 2019, 15, 2076–2084, doi:10.3762/bjoc.15.205

• starting material and the catalyst. Results and Discussion Our previous studies on α-photooxygenation of achiral aldehydes with 1O2 in the presence of chiral amines supported by DFT calculations indicate that the reaction is highly enantioselective only when both enamine structural fragments (substituents

1,2,3,4-Tetrahydro-1,4,5,8-tetraazaanthracene revisited: properties and structural evidence of aromaticity loss

• Arnault Heynderickx,
• Sébastien Nénon,
• Olivier Siri,
• Vladimir Lokshin and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2019, 15, 2059–2068, doi:10.3762/bjoc.15.203

• fluorescent. Minimum two Pekarian functions are needed to reproduce the band shape of the salts 6 in ethanol indicating that at least two electronic transitions are involved (Supporting Information File 1, Figure S3). TD DFT calculations interprets the longest wavelength absorption bands of 3 and 6 to be

• predominantly the charge transfer type HOMO -> LUMO transitions (Supporting Information File 1, Tables S1 and S2). The easiness of protonation and stability of salts 6 evidenced the behavior of THTAA (3) as a strong base. Indeed, our DFT calculations of the proton affinity of THTAA (3) produced ΔH298 = 235.9

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

• azobenzenes with different halogen bonding donor properties are discussed in relation to their changing photophysical properties, rationalized by DFT calculations. Keywords: azobenzene; DFT calculations; fluorine chemistry; halogen bonding; photochemistry; Introduction The halogen bond is an attractive

Reactions of 2-carbonyl- and 2-hydroxy(or methoxy)alkyl-substituted benzimidazoles with arenes in the superacid CF₃SO₃H. NMR and DFT studies of dicationic electrophilic species

• Dmitry S. Ryabukhin,
• Alexey N. Turdakov,
• Natalia S. Soldatova,
• Mikhail O. Kompanets,
• Alexander Yu. Ivanov,
• Irina A. Boyarskaya and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2019, 15, 1962–1973, doi:10.3762/bjoc.15.191

• -arylmethyl-substituted benzimidazoles, in yields up to 90%. The reaction intermediates, protonated species derived from starting benzimidazoles in TfOH, were thoroughly studied by means of NMR and DFT calculations and plausible reaction mechanisms are discussed. Keywords: benzimidazoles; cations; Friedel

• water. According to DFT calculations, protonation of the benzimidazole nitrogen N3 and the oxygen of the carbonyl or hydroxymethyl group in 1–8 leading to dicationic species I–III, V, VII, and VIII is thermodynamically favorable (−18.6 to −25.8 kcal/mol, Table 1). On the other hand, the dehydration of

• ). Summarizing all data obtained by DFT calculations (Table 1) and NMR studies (Table 2) of intermediate cations generated from benzimidazoles 1–8 in TfOH, and their reactions with arenes (Tables 3–5, Scheme 1, and Scheme 2), the following reaction mechanisms are proposed (Scheme 3 and Scheme 4). 2-Carbonyl

Inherent atomic mobility changes in carbocation intermediates during the sesterterpene cyclization cascade

• Hajime Sato,
• Takaaki Mitsuhashi,
• Mami Yamazaki,
• Ikuro Abe and
• Masanobu Uchiyama

Beilstein J. Org. Chem. 2019, 15, 1890–1897, doi:10.3762/bjoc.15.184

• 5/6/8/5 tetracyclic intermediate. This, in turn, is transformed to a 4/6-membered ring in quiannulatene biosynthesis, whereas 5/5 ring formation proceeds in sesterfisherol biosynthesis (Scheme 1, Scheme 2, and Scheme 3). Based on our DFT calculations, this regioselectivity is determined by the

Halide metathesis in overdrive: mechanochemical synthesis of a heterometallic group 1 allyl complex

• Ross F. Koby,
• Nicholas R. Rightmire,
• Nathan D. Schley,
• Timothy P. Hanusa and
• William W. Brennessel

Beilstein J. Org. Chem. 2019, 15, 1856–1863, doi:10.3762/bjoc.15.181

• this and several related points more quantitatively, various features of the K/Cs/[allyl]− system were modeled with DFT calculations, using the B3PW91 hybrid functional [27][28] with Grimme’s -D3 dispersion corrections (GD3BJ) [29]. A calculation on the simple model systems [K(C3H5)] and [Cs(C3H5

Complexation of 2,6-helic[6]arene and its derivatives with 1,1′-dimethyl-4,4′-bipyridinium salts and protonated 4,4'-bipyridinium salts: an acid–base controllable complexation

• Jing Li,
• Qiang Shi,
• Ying Han and
• Chuan-Feng Chen

Beilstein J. Org. Chem. 2019, 15, 1795–1804, doi:10.3762/bjoc.15.173

• derivatives for the additional multiple hydrogen bonding interactions between the hosts and the guests, which were evidenced by 1H NMR titrations, X-ray crystal structures and DFT calculations. Moreover, it was also found that the association constants (Ka) of the complexes could be significantly enhanced

• by the additional multiple hydrogen-bonding interactions between the hosts and the guests, which were evidenced by 1H NMR titration, X-ray crystal structures and DFT calculations. Moreover, we also found that the Ka values of the complexes could be significantly enhanced with larger counteranions of

• main reason for the formation of the stable complex H5·G1. DFT calculation of host–guest complexes To further investigate the complexation mode and structural characteristics of the host–guest complexes, DFT calculations were carried out at the B3LYP/6-31G level of theory for complex H4·G1 (Supporting

Functional panchromatic BODIPY dyes with near-infrared absorption: design, synthesis, characterization and use in dye-sensitized solar cells

• Quentin Huaulmé,
• Cyril Aumaitre,
• Outi Vilhelmiina Kontkanen,
• David Beljonne,
• Alexandra Sutter,
• Gilles Ulrich,
• Renaud Demadrille and
• Nicolas Leclerc

Beilstein J. Org. Chem. 2019, 15, 1758–1768, doi:10.3762/bjoc.15.169

• application in DSSCs, in rather good agreement with the values obtained from DFT calculations. Finally, we report preliminary results employing these molecules as photosensitizers in dye solar cells with iodine-based liquid electrolytes. We show that the limited performances of these new BODIPY derivatives

• DFT calculations In many opto-electronic devices the light-absorption properties of the semiconductors are a critical parameter. This is particularly the case when solar energy conversion applications are targeted. For instance, in order to maximize the photocurrent density in a DSSC device, the

• functional theory (TD-DFT) calculations on the four representative molecules displayed in Figure 2: Dyes (1 and 3) vs (2 and 4) differ by the position (2,6 or 1,7) of the methyl groups on the BODIPY core, while dyes (1 and 2) vs (3 and 4) differ by the presence (or not) of a triphenylamine donor group on the

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

• , Lippert–Mataga plots, cyclic voltammetry and density functional theory (DFT) calculations, we reveal the photophysical and electrochemical properties of the (D–π–)2A fluorescent dyes OUY-2, OUK-2 and OUJ-2. Results and Discussion Synthesis The (D–π–)2A fluorescent dyes OUY-2 [2], OUK-2 [3][4] and OUJ-2

• thiophene ring and the LUMO is mostly localized on the thienylpyridine moiety for OUY-2, the thienylpyrazine moiety for OUK-2 and the thienyltriazine moiety for OUJ-2 (Figure 6). Accordingly, the DFT calculations reveal that the photoexcitation of OUY-2, OUK-2 and OUJ-2 induces the ICT from the two

• OUJ-2 shows large bathochromic shifts of fluorescence maxima in polar solvents, as well as the Stokes shift values for OUJ-2 in polar solvents are much larger than those in nonpolar solvents. Cyclic voltammetry and DFT calculations demonstrated that the HOMO energy levels of the three dyes are

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• thermodynamic characteristics of β-CD hydration compare with those of its smaller α-cyclodextrin (α-CD) counterpart? In this study, we address these questions by employing a combination of experimental (DSC/TG) and theoretical (DFT) approaches. Keywords: β-cyclodextrin; DFT calculations; DSC/TG experiments

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

• Manuel Pedrón,
• Laura Legnani,
• Maria-Assunta Chiacchio,
• Pierluigi Caramella,
• Tomás Tejero and
• Pedro Merino

Beilstein J. Org. Chem. 2019, 15, 1552–1562, doi:10.3762/bjoc.15.158

• tetroxide-mediated oxidation of cyclopentane, tetrahydrofuran, tetrahydrothiophene and N-substituted pyrrolidines has been studied computationally by DFT and topological (analysis of the electron localization function, ELF) methods. In agreement with experimental observations and previous DFT calculations

• Waegell et al. proposed a new (3 + 2) asynchronous concerted mechanism [19][20], both groups converged to the latter proposed mechanism when Bakke et al. changed the interpretation of their kinetic isotopic experiments [21][22][23][24]. The (3 + 2) concerted mechanism was further confirmed by DFT

• calculations [25] which were also in agreement with the earlier experiments of Bakke et al. [15]. The computational study also confirmed the hydroxide adduct Ib as the active intermediate formed in the reaction. However, Petride et al. have demonstrated that iminium cations are intermediates in the RuO4

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• Cotton effect in this region [43][49]. If this is taken into account, it becomes obvious that the cis,cis-isomer adopts the M,M conformation. This is in line with the DFT calculations finding only the cis,cis-(M,M) isomer as minimum on the energy potential surface. The spectrum of cis,trans-10 allows the

Different reactivity of phosphorylallenes under the action of Brønsted or Lewis acids: a crucial role of involvement of the P=O group in intra- or intermolecular interactions at the formation of cationic intermediates

• Stanislav V. Lozovskiy,
• Alexander Yu. Ivanov and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2019, 15, 1491–1504, doi:10.3762/bjoc.15.151

• electrophilic activation with Brønsted or Lewis (super)acids, including reactions with arenes as π-nucleophiles, and investigation of intermediate cationic species by means of NMR and DFT calculations. Allenes used in this study are presented in Figure 1. We explored allenes having different substituents at the

• arenes toluene and xylenes (Table 3, entries 2–5). We carried out a DFT study [at the B3LYP/6-311+G(2d,2p) level of theory] for the observed AlCl3-involved reactions (Scheme 9, Scheme 10, Table 4 and Supporting Information File 1 for details of DFT calculations). First, the thermochemistry (ΔG of

• achieved. This reaction gave rise to phosphoryl-substituted alkenes and indanes. The intermediates of these reactions were investigated by means of NMR and DFT calculations, that shed light on the reaction mechanisms. Allenes 1a–j used in this study. 31P NMR monitoring of the progress of transformation of

Diazocine-functionalized TATA platforms

• Roland Löw,
• Talina Rusch,
• Fynn Röhricht,
• Olaf Magnussen and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1485–1490, doi:10.3762/bjoc.15.150

• trans-configurations and to predict thermodynamic and kinetic stabilities, we performed DFT calculations at the M06-2X/def2-TZVP level of theory (Table 1, for details see Supporting Information File 1, chapter VI). As expected for diazocine-based molecules our calculations predict the cis configuration

• activation energies (Ea) are calculated from the linear fit of an Arrhenius plot. Supporting Information Supporting Information File 526: Analytical methods, experimental procedures, NMR and UV spectra, kinetic studies and DFT calculations. Acknowledgements The authors gratefully acknowledge financial

Precious metal-free molecular machines for solar thermal energy storage

• Meglena I. Kandinska,
• Snejana M. Kitova,
• Vladimira S. Videva,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• Stanislav B. Baluschev,
• Silvia E. Angelova and
• Aleksey A. Vasilev

Beilstein J. Org. Chem. 2019, 15, 1096–1106, doi:10.3762/bjoc.15.106

• photoisomerization with lifetimes of the higher energy form longer than 500 seconds. Density functional theory (DFT) calculations at the B3LYP/6-31+G(d,p) level were performed in order to predict the enthalpies (H) of the cis and trans isomers and the storage energies (ΔH) for the systems studied. Keywords: aza-15

• density functional theory (DFT) calculations at the B3LYP/6-31+G(d,p) level. The first step in the molecular modelling investigation was the optimization of the molecular structures of the cis and trans isomers of dyes 4a–d (with the –(CH2)nSO3− (n = 3, 4) tails oriented to be in proximity to the aza-15

• the dyes and metal cations were obtained by density functional theory (DFT) calculations using the B3LYP functional [25][26] (the most often used functional for organic molecules and complexes) and the 6-31+G(d,p) [27][28][29] basis set for the lighter atoms (C, O, S, N, H) and SDD pseudopotential for

Molecular recognition using tetralactam macrocycles with parallel aromatic sidewalls

• Dong-Hao Li and
• Bradley D. Smith

Beilstein J. Org. Chem. 2019, 15, 1086–1095, doi:10.3762/bjoc.15.105

• (left) with anionic square planar metal halide complexes (right). (b) Solid-state structures of B·AuBr4− (X = CH, Z = t-Bu, left) and C·AuBr4− (X = CH, Z = t-Bu, right). (c) Electrostatic potential maps of the interior surfaces of (left) B and (right) C obtained by DFT calculations at the B3LYP/631G

An anomalous addition of chlorosulfonyl isocyanate to a carbonyl group: the synthesis of ((3aS,7aR,E)-2-ethyl-3-oxo-2,3,3a,4,7,7a-hexahydro-1H-isoindol-1-ylidene)sulfamoyl chloride

• Aytekin Köse,
• Aslı Ünal,
• Ertan Şahin,
• Uğur Bozkaya and
• Yunus Kara

Beilstein J. Org. Chem. 2019, 15, 931–936, doi:10.3762/bjoc.15.89

• release of carbon dioxide from the molecule. We performed theoretical computations to better understand the reaction mechanism shown in Scheme 4 (Figure 3). For this purpose, we employed density functional theory (DFT) calculations and performed geometric optimizations using the B3LYP functional [19][20

Mechanochemistry of supramolecules

• Anima Bose and
• Prasenjit Mal

Beilstein J. Org. Chem. 2019, 15, 881–900, doi:10.3762/bjoc.15.86

• solvent-assisted grinding using ethanol (Figure 25). The single crystal X-ray structures of the obtained co-crystals 44–46 were reported to match with the solution-phase co-crystals. They have also studied energy levels, thermal properties and the stability of these structures through DFT calculations