Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

• Eric W. Webb,
• Jonathan P. Moerdyk,
• Kyndra B. Sluiter,
• Benjamin J. Pollock,
• Amy L. Speelman,
• Eugene J. Lynch,
• William F. Polik and
• Jason G. Gillmore

Beilstein J. Org. Chem. 2019, 15, 2473–2485, doi:10.3762/bjoc.15.240

• functional theory (DFT) calculated molecular orbitals (MOs, e.g., Figure 6 and Supporting Information File 1) indicate that the LUMO (MO 106 for 3a) lies exclusively on the dienone moiety both in 1b and in the quinazolinespirohexadienone photochromes 3a,b. Thus, the dienone moiety is likely the electrophore

• deviation in the experimental measurements. This demonstrates that the computational correlation employed is useful in structural assignment and accurate within a standard of error of the experimental reduction potentials of these spirohexadienones’ different constitutional SW and LW isomers. Density

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

• -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

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

Aggregation-induced emission effect on turn-off fluorescent switching of a photochromic diarylethene

• Luna Kono,
• Yuma Nakagawa,
• Ayako Fujimoto,
• Ryo Nishimura,
• Yohei Hattori,
• Toshiki Mutai,
• Nobuhiro Yasuda,
• Kenichi Koizumi,
• Satoshi Yokojima,
• Shinichiro Nakamura and
• Kingo Uchida

Beilstein J. Org. Chem. 2019, 15, 2204–2212, doi:10.3762/bjoc.15.217

• functional theory (DFT) and time-dependent DFT (TDDFT). The excitation wavelengths as well as the emission wavelength qualitatively agrees with the experimental results. Since compound 1 consists of a diarylethene moiety and an imidazo[1,2-a]pyridine moiety, the characteristic of 1 has the combination of

• decreased gradually upon UV light irradiation accompanied with the formation of 1c, because of excitation energy transfer from the ESIPT moiety to the closed-ring isomer (Figure 5) [4]. The wavelengths of absorption (Table 3) and fluorescence (Table 4) were obtained computationally by using density

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• functional theory (DFT) to optimize the ground state equilibrium structures of (E)-2b, (Z)-2b, 8a and 8b, and used time-dependent DFT (TDDFT) and high-level correlated methods to obtain UV–vis absorption energies and oscillator strengths. To obtain the simulated absorption spectrum and λmax values

• ortho methyl groups in 2f, intramolecular photocyclization could be prevented. To verify the hypothetical structures derived from irradiation of 2b, we carried out quantum chemical calculations of the double bond isomers (E)-2b and (Z)-2b as well as the oxidized compounds 8a and 8b. We used density

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

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

• experimental) approaches are sometimes conflicting and contradictory. There is no “standard” method to investigate the complexation behavior of CDs. Thus, in our study a computational quantum mechanical modelling method, namely density functional theory (DFT) was chosen to investigate the electronic structure

Mechanochemical amorphization of chitin: impact of apparatus material on performance and contamination

• Thomas Di Nardo and
• Audrey Moores

Beilstein J. Org. Chem. 2019, 15, 1217–1225, doi:10.3762/bjoc.15.119

• systematic study of the effects of a number of medium parameters onto a model reaction, namely the amorphization of chitin where interchain stabilization is greater than 250 kJ/mol based on density functional theory (DFT) calculation [58]. We explored the role of the material of the jar and the ball, ball

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

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

A diastereoselective approach to axially chiral biaryls via electrochemically enabled cyclization cascade

• Hong Yan,
• Zhong-Yi Mao,
• Zhong-Wei Hou,
• Jinshuai Song and
• Hai-Chao Xu

Beilstein J. Org. Chem. 2019, 15, 795–800, doi:10.3762/bjoc.15.76

• moiety leads to the formation of 3a. Based on the proposed reaction mechanism and the results mentioned above, the cyclization of vinyl radical IV to give V is the atroposelective step. Density functional theory (DFT)-based calculations suggested that the cyclization of IV could be explained by a Curtin

Catalyst-free assembly of giant tris(heteroaryl)methanes: synthesis of novel pharmacophoric triads and model sterically crowded tris(heteroaryl/aryl)methyl cation salts

• Rodrigo Abonia,
• Luisa F. Gutiérrez,
• Braulio Insuasty,
• Jairo Quiroga,
• Kenneth K. Laali,
• Chunqing Zhao,
• Gabriela L. Borosky,
• Samantha M. Horwitz and
• Scott D. Bunge

Beilstein J. Org. Chem. 2019, 15, 642–654, doi:10.3762/bjoc.15.60

• over MgSO4, and concentrated under reduced pressure. Finally, the crystals were obtained after simple trituration with Et2O. Computational methods. Density functional theory (DFT) calculations were carried out with the Gaussian 09 program suite [66]. Geometries were fully optimized at the B3LYP [67][68

Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

• Ferran Planas,
• Michael J. McLeish and
• Fahmi Himo

Beilstein J. Org. Chem. 2019, 15, 145–159, doi:10.3762/bjoc.15.15

• the enzyme [19][20]. Thirty years later, density functional theory (DFT) calculations showed that the 4′-amino moiety of the cofactor can either accept or donate a proton in the reactions, depending on the protonation state of N1′ [21]. Orbital analysis of the IP/YIH+ reaction showed that full

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

Dispersion interactions

• Peter R. Schreiner

Beilstein J. Org. Chem. 2018, 14, 3076–3077, doi:10.3762/bjoc.14.286

• for all matter starting from atoms (e.g., the condensation of helium) over molecules (e.g., aggregation) to materials (e.g., adhesion). It is also difficult to include in theoretical approaches and for the longest time it had been left virtually unnoticed that many density functional theory (DFT

The activity of indenylidene derivatives in olefin metathesis catalysts

• Maria Voccia,
• Steven P. Nolan,
• Luigi Cavallo and
• Albert Poater

Beilstein J. Org. Chem. 2018, 14, 2956–2963, doi:10.3762/bjoc.14.275

• turnover event of an olefin metathesis reaction using a new family of homogenous Ru-based catalysts bearing modified indenylidene ligands has been investigated, using methoxyethylene as a substrate. The study is carried out by means of density functional theory (DFT). The indenylidene ligands are decorated

• [29][30][31]. We are interested in evaluating, by density functional theory (DFT) calculations, the difference in the activation step between complexes 1–6 in Scheme 1, whose reactivity and properties have been reported already (for 1 and 2) [24][32][33]. Predictive catalysis will be used here to

The influence of the cationic carbenes on the initiation kinetics of ruthenium-based metathesis catalysts; a DFT study

• Magdalena Jawiczuk,
• Angelika Janaszkiewicz and
• Bartosz Trzaskowski

Beilstein J. Org. Chem. 2018, 14, 2872–2880, doi:10.3762/bjoc.14.266

• . The excess positive charge of the quaternary ammonium is, in most cases, distributed over the imidazole core and mesityl groups and does not affect the ruthenium core nor the ruthenium–Ccarbene bond. Experimental We used density functional theory (DFT) using a computational protocol similar to our

Unprecedented nucleophile-promoted 1,7-S or Se shift reactions under Pummerer reaction conditions of 4-alkenyl-3-sulfinylmethylpyrroles

• Takashi Go,
• Akane Morimatsu,
• Hiroaki Wasada,
• Genzoh Tanabe,
• Osamu Muraoka,
• Yoshiharu Sawada and
• Mitsuhiro Yoshimatsu

Beilstein J. Org. Chem. 2018, 14, 2722–2729, doi:10.3762/bjoc.14.250

• key intermediate 15, of which the sulfanyl group would intramolecularly migrate to produce 16 stereoselectively (path c, not d). The hydrolysis of 16 using TBAH yields diol 17. We further confirmed the mechanism of the 1,7-S shift reaction by performing density functional theory (DFT)-based

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• adsorption of a molecule on a pre-covered surface using density functional theory (DFT) approaches with and without dispersion correction terms. In contrast to the above-mentioned intermediate-based selectivity, the steering-type interaction takes place before covalent bonds between molecule and surface are

A challenging redox neutral Cp*Co(III)-catalysed alkylation of acetanilides with 3-buten-2-one: synthesis and key insights into the mechanism through DFT calculations

• Andrew Kenny,
• Alba Pisarello,
• Arron Bird,
• Paula G. Chirila,
• Alex Hamilton and
• Christopher J. Whiteoak

Beilstein J. Org. Chem. 2018, 14, 2366–2374, doi:10.3762/bjoc.14.212

• procedure provides a wide substrate scope in terms of substituted acetanilides, although the optimised conditions were found to be more forcing than those for the corresponding benzamide substrates. Interestingly, density functional theory (DFT) studies reveal that the major impediment in the mechanism is

Hydroarylations by cobalt-catalyzed C–H activation

• Rajagopal Santhoshkumar and
• Chien-Hong Cheng

Beilstein J. Org. Chem. 2018, 14, 2266–2288, doi:10.3762/bjoc.14.202

• yields with anti-selectivity. The alkene product originally should be syn-13, but it rearranged to anti-13 at the high reaction temperature likely catalyzed by the cobalt complex. Moreover, the found intermolecular KIE of 1.4 and density functional theory (DFT) calculations strongly suggest that the

Water-soluble SNS cationic palladium(II) complexes and their Suzuki–Miyaura cross-coupling reactions in aqueous medium

• Alphonse Fiebor,
• Richard Tia,
• Banothile C. E. Makhubela and
• Henok H. Kinfe

Beilstein J. Org. Chem. 2018, 14, 1859–1870, doi:10.3762/bjoc.14.160

• parameterised for transition metal systems and has been found to give geometries, relative energies and activation energy trends in good agreement with high-level density functional theory (DFT) results at a fraction of the computational cost [45][46]. It is therefore adequate for studies in which the prime

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• -corrected density functional theory (DFT-D3) [44][45], spin-component-scaled approximated coupled cluster-singles-doubles (SCS-CC2) [46] as well as explicitly correlated local coupled cluster theory (LCCSD(T0)-F12) [47] calculations, the latter allowing for a quantification and visualization of London

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• density functional theory (DFT) computations, attractive LD forces were identified as the origin of this stability trend. Based on this study, LD interactions represent a valuable tool for the design of novel azobenzene photoswitches [24]. Herein we provide further evidence for the importance of LD as

Are dispersion corrections accurate outside equilibrium? A case study on benzene

• Tim Gould,
• Erin R. Johnson and
• Sherif Abdulkader Tawfik

Beilstein J. Org. Chem. 2018, 14, 1181–1191, doi:10.3762/bjoc.14.99

• interest in how to accurately model them. Multiple families of approaches for including dispersion forces in quantum chemical simulations now exist, mostly based around the principle of improving density functional theory (DFT) calculations (see, e.g., some key and recent summaries [3][5][13][14]) through

• polarisability tensor. Summary of modern dispersion methods Over the last decade, a number of new approaches have been developed that explicitly introduce dispersion forces into electronic structure theory methods – typically density functional theory (DFT). These approaches seek to overcome the fundamental lack