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

• the neighbouring adsorption site. This helps in understanding the nonstatistical pattern formation for this surface–adsorbate system and hints toward an inclusion of dispersion attraction as another determining factor for surface adsorption. Keywords: bonding analysis; cyclooctyne; density functional

• theory; dispersion; organic/inorganic interfaces; Introduction The creation of organic/inorganic interfaces is one of the main endeavours in enhancing the application range of modern electronic devices for silicon-based technology [1][2]. One way to achieve this is covalent attachment of bifunctional

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

Cobalt-catalyzed peri-selective alkoxylation of 1-naphthylamine derivatives

• Jiao-Na Han,
• Cong Du,
• Xinju Zhu,
• Zheng-Long Wang,
• Yue Zhu,
• Zhao-Yang Chu,
• Jun-Long Niu and
• Mao-Ping Song

Beilstein J. Org. Chem. 2018, 14, 2090–2097, doi:10.3762/bjoc.14.183

• previous literature [30][31][46][47], a plausible reaction mechanism for cobalt-catalyzed alkoxylation was proposed. As shown in Scheme 4, initially, CoIIX2 could be oxidized to CoIIIX2OR in the presence of a silver salt and an alcohol. Based on the experiments and the density functional theory

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

Cobalt-catalyzed C–H cyanations: Insights into the reaction mechanism and the role of London dispersion

• Eric Detmar,
• Valentin Müller,
• Daniel Zell,
• Lutz Ackermann and
• Martin Breugst

Beilstein J. Org. Chem. 2018, 14, 1537–1545, doi:10.3762/bjoc.14.130

• Abstract Carboxylate-assisted cobalt(III)-catalyzed C–H cyanations are highly efficient processes for the synthesis of (hetero)aromatic nitriles. We have now analyzed the cyanation of differently substituted 2-phenylpyridines in detail computationally by density functional theory and also experimentally

• intermediates and transition states. Keywords: catalysis; C–H activation; density functional theory; London dispersion; reaction mechanisms; Introduction For a long time, large and bulky substituents have intuitively been considered to act through unfavorable steric interactions, although London dispersion

• ligand dissociation process within the Pd(PPh3)4 system [25]. Furthermore, only the results obtained from dispersion-corrected density functional theory [28][29] were in agreement with the experimental observations and dispersion reduces the activation free energies by up to 30 kcal mol–1 [27]. Currently

Steric “attraction”: not by dispersion alone

• Ganna Gryn’ova and
• Clémence Corminboeuf

Beilstein J. Org. Chem. 2018, 14, 1482–1490, doi:10.3762/bjoc.14.125

• functional theory [39], post-Hartree–Fock [40][41], symmetry adapted perturbation theory (SAPT) [42][43][44][45][46] data or to a combination of the latter two (e.g., the monomer electron density force field, MEDFF) [47]. The latter approach has been subsequently exploited in the machine learning

• describing intermolecular interactions. Effective fragment potential (EFP) methods estimate it by adding a damping term to their classical multipolar expansion [36][37]. To account for this effect, quantum mechanically derived force fields (FFs) are fitted to semi-empirical [38], dispersion-corrected density

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• , anthracene and 1,5-dihydroxynaphthalene have been obtained at density functional theory level, using the M11 [42] exchange-correlation functional and the def2-TZVP [43] basis set implemented in the Gaussian 09 program package [44]. In order to take into account the solvent effect induced by the DMSO solvent

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

• quite poor, however, further reflecting their poorer treatment of dispersion energies and forces away from equilibrium. Conclusion In this work we used benchmark results for several configurations of the benzene dimer to test the ability of dispersion-corrected density functional theory to obtain

One hundred years of benzotropone chemistry

• Arif Dastan,
• Haydar Kilic and
• Nurullah Saracoglu

Beilstein J. Org. Chem. 2018, 14, 1120–1180, doi:10.3762/bjoc.14.98

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• enhance the induction energy. In a recent work by Hapka et al. it was shown that also standard density functional theory methods are able to describe nonadditive effects to the interaction energy quite well for hydrogen-bonded clusters, yet, fail to do so for dispersion bound complexes [31]. The common

Local energy decomposition analysis of hydrogen-bonded dimers within a domain-based pair natural orbital coupled cluster study

• Ahmet Altun,
• Frank Neese and
• Giovanni Bistoni

Beilstein J. Org. Chem. 2018, 14, 919–929, doi:10.3762/bjoc.14.79

• ]. They are typically carried out at the Hartree–Fock (HF) or density functional theory (DFT) level. In these schemes, the interacting system is treated as a supermolecule and the overall interaction energy is decomposed into various terms such as electrostatic interaction, charge transfer, polarization

Phosphodiester models for cleavage of nucleic acids

• Satu Mikkola,
• Tuomas Lönnberg and
• Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

An uracil-linked hydroxyflavone probe for the recognition of ATP

• Márton Bojtár,
• Péter Zoltán Janzsó-Berend,
• Dávid Mester,
• Dóra Hessz,
• Mihály Kállay,
• Miklós Kubinyi and
• István Bitter

Beilstein J. Org. Chem. 2018, 14, 747–755, doi:10.3762/bjoc.14.63

• complex were computed. Foremost, a molecular mechanical (MM) conformation analysis was performed for the individual molecules using the MMFF force field [47]. The stable conformers were optimized further at the density functional theory (DFT) level using the PBE functional [48][49] with D3BJ dispersion

D–A–D-type orange-light emitting thermally activated delayed fluorescence (TADF) materials based on a fluorenone unit: simulation, photoluminescence and electroluminescence studies

• Lin Gan,
• Xianglong Li,
• Xinyi Cai,
• Kunkun Liu,
• Wei Li and
• Shi-Jian Su

Beilstein J. Org. Chem. 2018, 14, 672–681, doi:10.3762/bjoc.14.55

• energy levels, are calculated from Ered and Eox. Compounds 1 and 2 have similar HOMO and LUMO energy levels due to the same donor and acceptor in the molecules (Table 1). The molecular geometry of 1 and 2 in the ground state and excited state were simulated by density functional theory (DFT) and time

• -dependent density functional theory (TD-DFT) calculations, respectively. The ground state (S0) geometries were optimized on B3LYP/6-31G* level in gas phase, while the lowest triplet excited state (T1) energy levels and the singlet excited state (S1) geometries of those molecules were optimized by TD-DFT on

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

• Ido Azuri,
• Anna Hirsch,
• Anthony M. Reilly,
• Alexandre Tkatchenko,
• Shai Kendler,
• Oded Hod and
• Leeor Kronik

Beilstein J. Org. Chem. 2018, 14, 381–388, doi:10.3762/bjoc.14.26

• . Keywords: density functional theory; THz spectroscopy; Introduction The transparency of many non-conductive materials in the terahertz range (0.1 to 10 THz) of the electromagnetic spectrum has led to the development of several potential applications of terahertz radiation [1]. Terahertz spectroscopy of

• yield reliable simulated spectra for complex materials is density functional theory (DFT) [23]. A significant complication, however, is that conventionally used exchange–correlation energy functionals in DFT do not describe the intermolecular dispersion interactions well. Therefore, early calculations

• Science, Tel Aviv University, Tel Aviv 6997801, Israel 10.3762/bjoc.14.26 Abstract We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene. Very good agreement with experimental data is found when using density functional

Recent advances on organic blue thermally activated delayed fluorescence (TADF) emitters for organic light-emitting diodes (OLEDs)

• Thanh-Tuân Bui,
• Fabrice Goubard,
• Malika Ibrahim-Ouali,
• Didier Gigmes and
• Frédéric Dumur

Beilstein J. Org. Chem. 2018, 14, 282–308, doi:10.3762/bjoc.14.18

• maintaining a large optical bandgap. In fact, dihedral angles of 49.9, 86.8, 71.4 and 82.4° were determined by density functional theory (DFT) calculations between the donor plane and the acceptor plane for T20–T23, respectively. Due to its lesser twisted structure and based on the design rule previously

Stereochemical outcomes of C–F activation reactions of benzyl fluoride

• Neil S. Keddie,
• Pier Alexandre Champagne,
• Justine Desroches,
• Jean-François Paquin and
• David O'Hagan

Beilstein J. Org. Chem. 2018, 14, 106–113, doi:10.3762/bjoc.14.6

• fluoride substrates (Figure 1), producing the corresponding substituted products in moderate to good yields. The water/isopropanol system was also shown to be amenable to phenolate and thiolate nucleophiles [3]. Previously, Paquin et al. undertook density functional theory (DFT) studies on the mechanism of

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• richer in bands than a typical ECD spectrum (just like IR spectra vs UV–vis spectra) [1][4][36]. Nowadays, density functional theory (DFT) allows a calculation of the VCD spectrum of a chiral molecule, which then can be compared with the measured VCD spectrum and by this the absolute configuration (AC

Halogen-containing thiazole orange analogues – new fluorogenic DNA stains

• Aleksey A. Vasilev,
• Meglena I. Kandinska,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• David Sucunza,
• Juan J. Vaquero,
• Obis D. Castaño,
• Stanislav Baluschev and
• Silvia E. Angelova

Beilstein J. Org. Chem. 2017, 13, 2902–2914, doi:10.3762/bjoc.13.283

• position) are presented in Figure 5 with the respective atom color scheme. The electronic reorganizations upon excitation were probed using time-dependent density functional theory (TDDFT) calculations. TDPBE0 (time-dependent density functional theory calculations using Perdew–Burke–Ernzerhof exchange

¹⁵N-Labelling and structure determination of adamantylated azolo-azines in solution

• Sergey L. Deev,
• Alexander S. Paramonov,
• Tatyana S. Shestakova,
• Igor A. Khalymbadzha,
• Oleg N. Chupakhin,
• Julia O. Subbotina,
• Oleg S. Eltsov,
• Pavel A. Slepukhin,
• Vladimir L. Rusinov,
• Alexander S. Arseniev and
• Zakhar O. Shenkarev

Beilstein J. Org. Chem. 2017, 13, 2535–2548, doi:10.3762/bjoc.13.250

• analysis in the 1D 13С spectra acquired with selective 15N decoupling, respectively. Additional spin–spin interactions were detected in the 15N-HMBC spectra. NMR data and DFT (density functional theory) calculations permitted to suggest a possible mechanism of isomerization for the adamantylated products

Pyrene–nucleobase conjugates: synthesis, oligonucleotide binding and confocal bioimaging studies

• Artur Jabłoński,
• Yannic Fritz,
• Hans-Achim Wagenknecht,
• Rafał Czerwieniec,
• Tytus Bernaś,
• Damian Trzybiński,
• Krzysztof Woźniak and
• Konrad Kowalski

Beilstein J. Org. Chem. 2017, 13, 2521–2534, doi:10.3762/bjoc.13.249

• using the density functional theory (DFT) with the hybrid gradient corrected correlation functional B3LYP [38] and Gaussian-type basis functions 6-311G(d,p) [39]. TD-DFT calculations were performed in the optimized ground state geometry using the same B3LYP functional and basis sets. Five lowest singlet