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

• -energy nπ* states are not present. This explanation is further substantiated using time-dependent density functional (TD-DFT) computations for pyrene–adenine conjugates 3 and 5. The molecular structures of compounds 3 and 5 were optimized at the B3LYP/6-311G(d,p) theory level. For the ground state

• geometry, ten excitations, five without spin flip and five to triplet excited states, respectively, were computed. The results for luminescence relevant transitions are summarized in Table 2. The TD-DFT computations predict, in particular, that the fluorescent state S1 of hydroxy compound 5 with the

• 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

Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

• Srikala Pangannaya,
• Neethu Padinchare Purayil,
• Shweta Dabhi,
• Venu Mankad,
• Prafulla K. Jha,
• Satyam Shinde and
• Darshak R. Trivedi

Beilstein J. Org. Chem. 2017, 13, 222–238, doi:10.3762/bjoc.13.25

• ]. The molecular geometry was fully optimized by using Berny’s optimization algorithm, which uses redundant internal coordinates. Molecular orbitals (HOMO, LUMO) were plotted using the GaussView software. In a second step the time-dependent DFT (TD-DFT) method was used considering the same B3LYP exchange

• a first order rate equation for the anion binding process. 1H NMR and TD-DFT calculations further confirmed the anion binding process of receptor R1 and R2 with F− and AcO− ions. The detection ability of Hg2+ and F− ions by receptor R1 allows its usage in molecular logic gate applications

Characterization of the synthetic cannabinoid MDMB-CHMCZCA

• Carina Weber,
• Stefan Pusch,
• Dieter Schollmeyer,
• Sascha Münster-Müller,
• Michael Pütz and
• Till Opatz

Beilstein J. Org. Chem. 2016, 12, 2808–2815, doi:10.3762/bjoc.12.279

• CO and/or a cyclohexyl radical or methylenecyclohexane. As MDMB-CHMCZCA bears a stereogenic center at C-1', the elucidation of the absolute configuration of the sample was attempted by ECD spectroscopy. While the UV spectra can be adequately predicted by TD-DFT calculations (time-dependent density

• TD-DFT; however, the experimental positive/negative sequence is inverted in the range from 200 to 230 nm. Overall, this yields an enantiomeric similarity index (ESI) [16] of only 34% in favor of the S-enantiomer, therefore not enabling a reliable assignment of the absolute configuration. The

• kcal/mol were selected from this set, the structures were confirmed as local minima (no imaginary frequencies), and the geometries were used for the excited-state calculations. ECD spectra were calculated using TD-DFT (number of states: 75) at the TD- and TDA-B3LYP/6-311++G** [23][24][25][26][27][28

Benzothiadiazole oligoene fatty acids: fluorescent dyes with large Stokes shifts

• Lukas J. Patalag and
• Daniel B. Werz

Beilstein J. Org. Chem. 2016, 12, 2739–2747, doi:10.3762/bjoc.12.270

• (d,p)) reveal that the HOMO is predominantly located at the oligoene chain while the LUMO is rather spread over the BTD terminus (Figure 3). Indeed, further TD-DFT calculations (not shown) assign the longest wavelength absorptions of all three compounds to a high contribution of a HOMO–LUMO

High performance p-type molecular electron donors for OPV applications via alkylthiophene catenation chromophore extension

• Paul B. Geraghty,
• Calvin Lee,
• Jegadesan Subbiah,
• Wallace W. H. Wong,
• James L. Banal,
• Mohammed A. Jameel,
• Trevor A. Smith and
• David J. Jones

Beilstein J. Org. Chem. 2016, 12, 2298–2314, doi:10.3762/bjoc.12.223

• -dependent DFT (TD-DFT) calculations were carried out on the optimized structures with PBE0/def2-TZVP level of theory based on our benchmark calculations (Supporting Information File 1, chapter S11). It is apparent in Figure 11 that as the BXR molecular materials increase in size the overlap of the HOMO and

New furoisocoumarins and isocoumarins from the mangrove endophytic fungus Aspergillus sp. 085242

• Ze’en Xiao,
• Senhua Chen,
• Runlin Cai,
• Shao’e Lin,
• Kui Hong and
• Zhigang She

Beilstein J. Org. Chem. 2016, 12, 2077–2085, doi:10.3762/bjoc.12.196

• R1 values were 0.0350, ωR2 = 0.0899 (I > 2σ(I)). The goodness of fit on F2 was 1.067. CCDC number: 1458040. Calculation of ECD spectra. Molecular Merck force field (MMFF) and DFT/TD-DFT calculations were carried out with Spartan’ 14 software (Wavefunction Inc., Irvine, CA, USA) and Gaussian 09

Thiophene-forming one-pot synthesis of three thienyl-bridged oligophenothiazines and their electronic properties

• Dominik Urselmann,
• Konstantin Deilhof,
• Bernhard Mayer and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2016, 12, 2055–2064, doi:10.3762/bjoc.12.194

• oligophenothiazines. TD-DFT and even semiempirical ZINDO calculations reproduce the trends of longest wavelengths absorption bands and allow the assignment of these transitions to possess largely charge-transfer character from the adjacent phenothiazinyl moieties to the central thienyl unit. Keywords: C–C coupling

• oligophenothiazines [45]. With these geometry-optimized structures in hand the electronic absorptions were calculated with the semiempirical ZINDO-CI, and TD-DFT (B3LYP and CAM-B3LYP, an implemented hybrid exchange-correlation functional [81], using the polarizable continuum model (PCM) [82] applying dichloromethane

• terphenothiazinyl moieties to the thienyl bridge, in the TD-DFT methods significant contributions of HOMO-2 to LUMO transitions contribute to the corresponding S1 states. The inspection of the Kohn–Sham FMOs, contributing to the S1 states and representing the longest wavelength absorption bands, indicates that the

On the mechanism of imine elimination from Fischer tungsten carbene complexes

• Philipp Veit,
• Christoph Förster and
• Katja Heinze

Beilstein J. Org. Chem. 2016, 12, 1322–1333, doi:10.3762/bjoc.12.125

• first-order rate-law with a Gibbs free energy of activation of ΔG‡298K = 112 kJ mol−1. Three proposed mechanistic pathways are taken into account and supported by detailed (time-dependent) densitiy functional theory [(TD)-DFT] calculations. The preferred pathway is initiated by an irreversible CO

• ) followed by detailed mechanistic studies regarding the formation of imine E-3 are presented including mass spectrometric, NMR, IR and UV–vis spectroscopic kinetic studies in combination with (TD)-DFT methods. Results and Discussion Synthesis of W(CO)5(E-2) The diferrocenyl NH carbene complex W(CO)5(E-2) is

• the calculated TD-DFT spectrum of imine E-3 (Supporting Information File 1, Figure S29). All spectroscopic and analytical data suggest that the imine formation is faster than the CO dissociation. Conclusion The thermally induced formation of E-1,2-diferrocenylimine E-3 from the NH carbene

Three new trixane glycosides obtained from the leaves of Jungia sellowii Less. using centrifugal partition chromatography

• Luíse Azevedo,
• Larissa Faqueti,
• Marina Kritsanida,
• Antonia Efstathiou,
• Despina Smirlis,
• Gilberto C. Franchi Jr,
• Grégory Genta-Jouve,
• Sylvie Michel,
• Louis P. Sandjo,
• Raphaël Grougnet and
• Maique W. Biavatti

Beilstein J. Org. Chem. 2016, 12, 674–683, doi:10.3762/bjoc.12.68

• using density functional theory (DFT) at the B3LYP/6-311+g (d,p) level of theory. A check for imaginary frequencies was performed in order to confirm the presence of a real minimum. Calculations of the rotational strengths and excitation energies were realized using time dependent (TD) DFT at the same

Chiroptical properties of 1,3-diphenylallene-anchored tetrathiafulvalene and its polymer synthesis

• Masashi Hasegawa,
• Junta Endo,
• Seiya Iwata,
• Toshiaki Shimasaki and
• Yasuhiro Mazaki

Beilstein J. Org. Chem. 2015, 11, 972–979, doi:10.3762/bjoc.11.109

• using TD-DFT calculations [21]. Thus, the intensive Cotton effect is associated with the exciton coupling of the two chromophores of the iodobenzene units. In the ECD spectrum of (+)-9, the mirror image of the trend lines of (−)-9 was found. The UV–vis absorption spectrum of 3 exhibits absorption maxima

• at 314 and 405 nm. In the ECD spectra of (+)/(−)-3, the Cotton effect was observed over the entire absorption range. A simulated spectrum of 3 with the (R)-configuration, calculated by TD-DFT (B3LYP/6-31G(d,p)), has moderate resemblance to the spectrum obtained from (−)-3. This result is also

• validation of the absolute configurations based on the TD-DFT method. Although the observed Cotton effect associated with TTF moieties is relatively weak, each chiral allene is stable towards the racemization under ambient light. A chiral copolymer based on TTF and a chiral 1,3-diphenylallene as the main

Carboxylated dithiafulvenes and tetrathiafulvalene vinylogues: synthesis, electronic properties, and complexation with zinc ions

• Yunfei Wang and
• Yuming Zhao

Beilstein J. Org. Chem. 2015, 11, 957–965, doi:10.3762/bjoc.11.107

• -dependent density functional theory (TD-DFT) calculations (see the Supporting Information File 1 for details). The UV–vis data indicates that the degrees of π-delocalization for the TTFVs and DTF compounds are quite similar. This result is congruous with the fact that diphenyl-TTFVs generally prefer a

• , thermal gravimetric analysis (TGA) data of 8, and time-dependent (TD) DFT calculation results for compounds 6 and 7. Acknowledgements We thank the Natural Sciences and Engineering Research Council (NSERC) of Canada, Canada Foundation for Innovation (CFI), and Memorial University for financial support.

Trifluoromethyl-substituted tetrathiafulvalenes

• Olivier Jeannin,
• Frédéric Barrière and
• Marc Fourmigué

Beilstein J. Org. Chem. 2015, 11, 647–658, doi:10.3762/bjoc.11.73

• trifluoromethyl-substituted TFF derivatives are lightly orange colored, while the ester and cyano TTFs are dark red compounds. In order to rationalize these evolutions, we have performed TD-DFT calculations on the model molecules TTF, TTF-CF3, TTF-CO2Me and TTF-CN. The results are shown in Figure 2 and collected

• initial geometry optimization calculations. Final geometries are given in Supporting Information File 1. Representation of frontier orbitals included in Figure 2 were generated with Molekel 4.3 [57]. TD-DFT calculations were performed at the B3LYP/6-311G** level of theory, on the previously converged

• optical transitions deduced from TD-DFT calculations (see Table 3). View of the 2ac molecule. Thermal ellipsoids are shown at the 50% probability level. View of the 2bc molecule. Thermal ellipsoids are shown at the 50% probability level. View of the two crystallographically independent 4bc molecules

Scalable synthesis of 5,11-diethynylated indeno[1,2-b]fluorene-6,12-diones and exploration of their solid state packing

• Bradley D. Rose,
• Peter J. Santa Maria,
• Aaron G. Fix,
• Chris L. Vonnegut,
• Lev N. Zakharov,
• Sean R. Parkin and
• Michael M. Haley

Beilstein J. Org. Chem. 2014, 10, 2122–2130, doi:10.3762/bjoc.10.219

• which has previously and incorrectly been described as an n→π* transition [16][20]; however, TD-DFT calculations predict this to be π→π* (Figure 3) [27][28]. The n→π* transition was calculated to have a slightly higher energy transition with an oscillator strength of 0; thus, it should not be visible in

Columnar/herringbone dual crystal packing of pyrenylsumanene and its photophysical properties

• Binod Babu Shrestha,
• Shuhei Higashibayashi and
• Hidehiro Sakurai

Beilstein J. Org. Chem. 2014, 10, 841–847, doi:10.3762/bjoc.10.80

• maximum of 1 was evidently red-shifted relative to those of 3 and pyrene. The 355 nm absorption band of 1 was assigned to the HOMO–LUMO transition by TD-DFT calculations (ωB97XD/6-31G(d)). DFT calculations also demonstrated that the HOMO and LUMO of 1 are primarily located on the pyrene moiety (Figure 4

One-pot three-component synthesis and photophysical characteristics of novel triene merocyanines

• Christian Muschelknautz,
• Robin Visse,
• Jan Nordmann and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 599–612, doi:10.3762/bjoc.10.51

• -en-1-ylideneindolones are essentially nonemissive in films or in the solid state. TD-DFT computations rationalize the charge-transfer nature of the characteristic broad long-wavelength absorptions bands. Keywords: alkynes; cross coupling; enamines; fluorescence; heterocycles; multicomponent

• frequency analysis. The optimized structure of 10a was submitted to a TD-DFT calculation for assigning the experimentally determined absorption characteristics (Table 5). Therefore, the hybrid exchange–correlation functional CAM-B3LYP [58] was implemented and a non-equilibrium solvation [59][60][61][62][63

• of the 1-styryleth-2-enylidene indolones 8 and the 4-(1,3,3-trimethylindolin-2-ylidene)but-2-en-1-ylidene indolones 10. Experimental and TD-DFT computed (CAM-B3LYP 6-311G(d,p)) absorption maxima of the 4-(1,3,3-trimethylindolin-2-ylidene)but-2-en-1-ylideneindolone 2E,4Z,6Z-10a. Supporting

Photoionisation of the tropyl radical

• Kathrin H. Fischer,
• Patrick Hemberger,
• Andras Bodi and
• Ingo Fischer

Beilstein J. Org. Chem. 2013, 9, 681–688, doi:10.3762/bjoc.9.77

• calculated the EOM-CCSD/cc-pVTZ excitation energies for the triplet states, using QChem 4 [44] at the DFT-optimised ground state tropyl ion geometry, to be 3.82 and 4.00 eV, corresponding to 10.05 and 10.23 eV photon energies. TD-DFT calculations yield 9.70, 10.05 eV (B3LYP/6-311++G(d,p)); 9.86, 10.25 (M06

• . The shoulder at around 10.7 eV in Figure 4 might be tentatively assigned to this state. However, previous calculations predicted the first singlet excited state at photon energies of 11.3 [9] and 11.74 eV [45]. Our EOM-CCSD result at 11.07 and TD-DFT results at 11.09, 11.24 and 10.95 eV with the B3LYP

• by a 1 eV gap to the next electronic excited state. EOM-CCSD vertical-excitation-energy calculations predict that the next higher lying state is a triplet at 12.48 eV followed by two more triplet states in ca. 100 meV intervals as well as several singlet states around 12.8 eV. TD-DFT calculations, on

Toward unidirectional switches: 2-(2-Hydroxyphenyl)pyridine and 2-(2-methoxyphenyl)pyridine derivatives as pH-triggered pivots

• Christina Tepper and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2012, 8, 977–985, doi:10.3762/bjoc.8.110

• density functional theory (TD-DFT) with the B3LYP functional and by employing the 6-31G* basis set. The absorption band at 290 nm for the 3-methylpyridine 7 as well as the absorption band at 331 nm for the protonated 3-methylpyridine 8 are dominated by the transition of an electron from the HOMO to the

• (TD-DFT) with B3LYP as a functional and by employing the 6-31G* basis set (Figure 6b). TD-DFT calculations were performed at the optimized ground-state geometries of (M)-13 and (P)-13, calculating the energy, oscillator strength and rotatory strength for each of the 200 lowest singlet excitations. The

• unidirectionally. Another result is found for the switch 10: If we compare the simulated spectra of (M)-10 and (P)-10, using time-dependent density functional theory (TD-DFT-B3LYP/6-31G*; Figure 7b) with the measured spectrum of 10 in DCM (Figure 7a), it becomes evident that the M isomer is the prevailing one. The

Synthesis, solid-state fluorescence properties, and computational analysis of novel 2-aminobenzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides

• Kenichirou Yokota,
• Masayori Hagimori,
• Naoko Mizuyama,
• Yasuhisa Nishimura,
• Hiroshi Fujito,
• Yasuhiro Shigemitsu and
• Yoshinori Tominaga

Beilstein J. Org. Chem. 2012, 8, 266–274, doi:10.3762/bjoc.8.28

• ; H, 4.32; N, 16.11. (a) HOMO and (b) LUMO for 3a, computed with TD-DFT(B3LYP)/6-31+G(d,p). The pink (blue) lobes indicate a positive (negative) isocontour value of 0.03. The distribution of the HOMO minus LUMO density for 3a, computed with TD-DFT(B3LYP)/6-31+G(d,p). The pink (blue) lobes indicate a

The arene–alkene photocycloaddition

• Ursula Streit and
• Christian G. Bochet

Beilstein J. Org. Chem. 2011, 7, 525–542, doi:10.3762/bjoc.7.61

• UV absorption band at 380 nm was observed. This absorption band fits well with TD-DFT calculations. He proposes that re-aromatization of this intermediate takes place via a zwitterionic species or through a proton catalyzed pathway. We recently found in our laboratories that the intramolecular

Predicting the UV–vis spectra of oxazine dyes

• Scott Fleming,
• Andrew Mills and
• Tell Tuttle

Beilstein J. Org. Chem. 2011, 7, 432–441, doi:10.3762/bjoc.7.56

• Scott Fleming Andrew Mills Tell Tuttle WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK 10.3762/bjoc.7.56 Abstract In the current work we have investigated the ability of time-dependent density functional theory (TD-DFT) to

• ; oxazine; TD-DFT; UV–vis; Introduction Oxazine dyes are a subclass of quinone imines, which are all based upon the p-benzoquinone imine or -diimine scaffold. Other important subclasses within the quinone imines include, the azine dyes and thiazine dyes. The structural relationships described are

• observations by a computational study of the solvatochromism of the oxazine dye Nile red [12]. In the investigation, TD-DFT was applied in order to try and explore the contributing factors in the solvatochromism observed with Nile red, upon gradually increasing the solvent polarity from benzene to acetonitrile

Syntheses and properties of thienyl-substituted dithienophenazines

• Annemarie Meyer,
• Eva Sigmund,
• Friedhelm Luppertz,
• Gregor Schnakenburg,
• Immanuel Gadaczek,
• Thomas Bredow,
• Stefan-S. Jester and
• Sigurd Höger

Beilstein J. Org. Chem. 2010, 6, 1180–1187, doi:10.3762/bjoc.6.135

• : oligothiophenes; phenazines; scanning tunneling microscopy; self-assembled monolayers; TD-DFT calculations; Introduction Thiophene based oligomers and polymers have drawn considerable interest as active materials in various fields of organic electronics such as organic light-emitting diodes (OLEDs), organic thin

• therefore be expected that at room temperature all conformations are present. For simplicity we only present results for the most stable structure. For the treatment of excited states time-dependent density functional theory (TD-DFT) was applied. The COSMO model was used to simulate the solution environment

• of the absorption and emission spectra. Spectral data of oligothiophenes in CH2Cl2.. Lowest vertical excitation energies obtained by B3LYP/TZVP TD-DFT calculations of the quaterthiophene 19 and derivatives as well as sexithiophene 20 and derivatives (gas phase and in CH2Cl2) in eV, and oscillator

Intramolecular hydroxycarbene C–H-insertion: The curious case of (o-methoxyphenyl)hydroxycarbene

• Dennis Gerbig,
• David Ley,
• Hans Peter Reisenauer and
• Peter R. Schreiner

Beilstein J. Org. Chem. 2010, 6, 1061–1069, doi:10.3762/bjoc.6.121

• that this compound was not present among the pyrolysis products. Even after more than 12 h in the dark at 11 K, the IR spectrum was unchanged, indicating that there is no compound among the pyrolysis products that is susceptible to a tunneling decay mechanism. The TD-DFT (B3LYP/cc-pVDZ) absorption

An enantiomerically pure siderophore type ligand for the diastereoselective 1 : 1 complexation of lanthanide(III) ions

• Markus Albrecht,
• Olga Osetska,
• Thomas Abel,
• Gebhard Haberhauer and
• Eva Ziegler

Beilstein J. Org. Chem. 2009, 5, No. 78, doi:10.3762/bjoc.5.78

• should be the only C3-symmetric isomer present in solution. As further evidence that the formation of the 1·La complex is strictly diastereoselective the UV and CD spectra of the (Λ2)-1b·La complex were simulated on the basis of time-dependent density functional theory (TD-DFT) with the PBE1PBE

• functional and by employing the LANL2DZ basis set [37]. TD-DFT calculations were performed at the optimized ground-state geometry (B3LYP/LANL2DZ), calculating the energy, oscillator strength and rotatory strength for each of the 200 lowest singlet excitations. The CD spectrum was simulated by overlapping

• : calculated spectrum of the Λ2 isomer of complex 1b·La calculated at the TD-DFT-PBE1PBE/LANL2DZ level. Preparation of the compound 1a-H3 by utilization of a multiple Claisen-rearrangement. Acknowledgments This work was supported by the DFG (SPP 1166) and the Fonds der Chemischen Industrie.