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 pyrene in comparison with 1,5-dihydroxynaphthalene are somewhat in contradiction with the molecular modelling results obtained in the gas phase. However, the influence of DMSO as the solvent on the dihydroxylated guest is more pronounced than on the aromatic hydrocarbons. This stronger 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

• kcal mol−1 for 5–7, respectively, relative to the lowest energy conformer) were then re-optimized at the B3LYP/6-31G** [26][27][28][29] level of theory with and without D3(BJ) [30][31] dispersion correction (gas phase) (conformations of one enantiomer of each diastereomer of 4 were analyzed. The

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

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

• gas phase. The experimentally determined ionization potential of an isolated water molecule was used (0.4638 Eh [62][63]). LED analysis in the DLPNO-CCSD(T) framework The theory and implementation of the DLPNO-CCSD(T) method and of the LED scheme have been described in detail in a series of recent

Biocatalytic synthesis of the Green Note trans-2-hexenal in a continuous-flow microreactor

• Morten M. C. H. van Schie,
• Tiago Pedroso de Almeida,
• Gabriele Laudadio,
• Florian Tieves,
• Elena Fernández-Fueyo,
• Timothy Noël,
• Isabel W. C. E. Arends and
• Frank Hollmann

Beilstein J. Org. Chem. 2018, 14, 697–703, doi:10.3762/bjoc.14.58

• an oxidation reaction dissolved O2 is consumed rapidly and diffusion of O2 into the reaction medium can easily become overall rate-limiting. The O2 diffusion rate into the reaction medium directly correlates with the interfacial area between aqueous medium and the gas phase. Large interfacial surface

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

• -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

• a Keithley 2420 and Konica Minolta chromameter CS-200. The EL spectra were measured with a Photo Research PR705 device. (a) The optimized S0 geometries of 1 (left) and 2 (right) on B3LYP/6-31G* level in gas phase; (b) The frontier molecular orbital distributions of 1 and 2; (c) The optimized S1

• simulated EQE by employing the TTA model. Molecular structures of isomers 1 and 2. Thermal and electrochemical properties of the investigated compounds 1 and 2. The calculated HOMO, LUMO, twisting angles (θ, θ’), bond lengths (l, l’), ΔEST and dipole moment in gas phase for S0 and in solution for S1, from

Conformational preferences of α-fluoroketones may influence their reactivity

• Graham Pattison

Beilstein J. Org. Chem. 2017, 13, 2915–2921, doi:10.3762/bjoc.13.284

• -haloacetophenone, calculating the energy of each compound as the carbon–halogen bond is rotated through 10° increments in both the gas phase and in ethanol as reaction solvent (Figure 1) [10]. The fluorinated acetophenone showed significant differences in conformational energy to the chlorinated and brominated

• variants. The energy minimum for α-fluoroacetophenone was displayed at an O=C–C–X dihedral angle of around 140° in the gas phase, whilst the chloro- and bromoacetophenones both showed minima around 110°. Highly polar conformations which place the C–X bond in the same plane as the carbonyl group were

• smaller dihedral angle preferred by the chlorinated derivative in the gas phase. Figure 3 compares the lowest energy conformations of α-fluoroacetophenone and α-chloroacetophenone in the polar solvent ethanol. Experimental work by Olivato amongst others supports these conformational preferences [11][12

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• [10][25]. A comparison of this cisoid base pair with its transoid counterpart (Scheme 4b) suggests that the latter geometry may be additionally stabilized by a synergistic hydrogen bond. Indeed, computations indicate that the transoid base pair is favoured by 7.6 kcal mol−1 in the gas phase [57]. It

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

• compound 15a. To evaluate the relative thermodynamic stabilities of isomers 15a,b and 21a,b, we performed DFT calculations with the RB3LYP/6-31-G(d,p) approximation in the gas phase using the Gaussian 09 package [40]. Isomers 15b and 21b are thermodynamically more stable than counterparts 15a and 21a. The

Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity

• Tathagata Mukherjee,
• Soumik Biswas,
• Andreas Ehnbom,
• Subrata K. Ghosh,
• Ibrahim El-Zoghbi,
• Nattamai Bhuvanesh,
• Hassan S. Bazzi and
• John A. Gladysz

Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246

• group, and these are treated in the discussion section. In order to help interpret the accessibilities and/or stabilities of the various iodine(III) dichlorides described above, the gas phase free energies of chlorination were computed by DFT methods as described in the experimental section and

• 119.6(2), C6–C5–C13 119.3(2), average of 8 CF–CF–CF 115.0(10). Ball-and-stick and space filling representations of the unit cell of 1,3,5-(Rf6)2C6H3I. Free energies of chlorination of relevant aryl and alkyl iodides to the corresponding iodine(III) dichlorides in the gas phase (kcal/mol), presented in a

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• and Br atoms. Iodine atoms were modeled by the Stuttgart−Dresden (SDD) pseudopotential and the accompanying SDD basis set [57]. Full geometry optimization in the gas phase was followed by vibrational frequency calculations that identified calculated stationary points as minima. Calculated Raman

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• gas phase, in solution and in the solid state. Mass spectrometry was employed for the investigation of the architecture and relative gas-phase stabilities of these supramolecular complexes. The mode of complexation was further tracked by 1D and 2D NMR proving the formation of the exclusion-type

• ; pemetrexed; supramolecular chemistry; Introduction Herein, supramolecular host–guest complexes of the potent folic acid inhibitor pemetrexed (PTX, Figure 1a) with native cyclodextrins (α-, β- and γ-CDs, Figure 1b) in the gas phase (MS), in solution (NMR, UV–vis) and in the solid state (Raman, FTIR–ATR) were

• CDs/PTX complexes were examined in terms of complex stability in gas-phase collision induced dissociation (CID) experiments using mass spectrometry (MS). This approach provides insight into the intrinsic features of these noncovalently associated molecules, i.e., without the presence, and hence

Complexation of molecular clips containing fragments of diphenylglycoluril and benzocrown ethers with paraquat and its derivatives

• Leonid S. Kikot',
• Catherine Yu. Kulygina,
• Alexander Yu. Lyapunov,
• Svetlana V. Shishkina,
• Roman I. Zubatyuk,
• Tatiana Yu. Bogaschenko and
• Tatiana I. Kirichenko

Beilstein J. Org. Chem. 2017, 13, 2056–2067, doi:10.3762/bjoc.13.203

• approved earlier and described in our previous studies [29][30]. FAB–MS is known as a versatile method to detect supramolecular complexes from solutions after transferring them into the gas phase [31][32]. The solutions containing equimolar amounts of clips 1–5 and paraquat (7) in 3-nitrobenzyl alcohol

New bio-nanocomposites based on iron oxides and polysaccharides applied to oxidation and alkylation reactions

• Daily Rodríguez-Padrón,
• Alina M. Balu,
• Antonio A. Romero and
• Rafael Luque

Beilstein J. Org. Chem. 2017, 13, 1982–1993, doi:10.3762/bjoc.13.194

• . Once the references were obtained, the acquisition of the spectra was carried out starting with the lowest temperature. Pyridine (PY) and 2,6-dimethylpyridine (DMPY) titration Pyridine (PY) and 2,6-dimethylpyridine (DMPY) titration experiments were carried out at 300 °C, via gas phase adsorption of the

Conformational impact of structural modifications in 2-fluorocyclohexanone

• Francisco A. Martins,
• Josué M. Silla and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2017, 13, 1781–1787, doi:10.3762/bjoc.13.172

• interaction with the carbonyl oxygen or by electron delocalization (hyperconjugation) involving the good electron acceptor π*C=O orbital. For example, 2-fluorocyclohexanone in the gas phase exists predominantly in the axial conformation, but the equatorial form is more stable in solution [18]. In a previous

• to evaluate the interactions controlling the conformational equilibriums and to obtain insight on the spectroscopic (NMR) behavior of the studied compounds (Figure 1). Results and Discussion The axial population of 2-fluorocyclohexanone in the gas phase has been found to be 64%, decreasing to only 2

• DMSO solution relative to the gas phase only in compounds with Y = CH2 (the population does not vary with the solvent when X = CH2 and NHax). In these cases, the axial conformer has similar or larger molecular dipole moments than the equatorial form (differently from the other compounds). In addition

New electroactive asymmetrical chalcones and therefrom derived 2-amino- / 2-(1H-pyrrol-1-yl)pyrimidines, containing an N-[ω-(4-methoxyphenoxy)alkyl]carbazole fragment: synthesis, optical and electrochemical properties

• Daria G. Selivanova,
• Alexei A. Gorbunov,
• Olga A. Mayorova,
• Alexander N. Vasyanin,
• Igor V. Lunegov,
• Elena V. Shklyaeva and
• Georgii G. Abashev

Beilstein J. Org. Chem. 2017, 13, 1583–1595, doi:10.3762/bjoc.13.158

• comparison with the ground state takes place, as evidenced by the quantum-chemical calculations carried out with the help of the Fire Fly package [30][31] on a PGU Tesla supercomputer. All calculations of the dipole moments, HOMO and LUMO energies were performed on the B3LYP/6-31G* level for the gas phase

• -carbaldehydes 2a,b and 1-(5-arylthiophen-2-yl)ethanones 5a,b. Synthesis of quadrupolar chromophores 6a,b−8a,b. Physicochemical characteristics of compounds 2a,b−8a,b. The values of the dipole moments in the ground (μ0) and excited (μ*) states, the frontier orbitals energies and the absorption maxima in the gas

• phase and in various solvents calculated by B3LYP/6-31G* and TD-B3LYP/6-31G* methods for compound 6a. Electrochemical characteristics of compounds 6–8 versus Fc/Fc+. Supporting Information Supporting Information File 134: Synthetic procedures and characterization data for all compounds 1–8 (a,b

Correlation of surface pressure and hue of planarizable push–pull chromophores at the air/water interface

• Frederik Neuhaus,
• Fabio Zobi,
• Gerald Brezesinski,
• Marta Dal Molin,
• Stefan Matile and
• Andreas Zumbuehl

Beilstein J. Org. Chem. 2017, 13, 1099–1105, doi:10.3762/bjoc.13.109

• values as before depicting a stably organized monolayer film with possible long-range order. The area per molecule of about 38 Å2 is comparable to that observed for cholesterol monolayers [21][22]. Simulation The molecular geometry of the mechanosensitive flipper probe was simulated in the gas phase at

• . Computational simulations Geometry optimization, as well as frequency calculations for the flipper mechanophore, were performed in the gas phase at the density functional level of theory with the Gaussian 03 program package [35] using the hybrid B3LYP functional [36] in conjunction with the LanL2DZ basis set

• groups (h) and b) measuring the distance d between centroids of planes defined by the outmost external atoms with A = π(d/2)2. In the gas phase optimized geometry d = 6.88 Å giving A = 37.2 Å2. However, by assuming free rotation around the C–C bond connecting the two dithienothiophene units a maximum

Conformational study of L-methionine and L-cysteine derivatives through quantum chemical calculations and ³J_HH coupling constant analyses

• Weslley G. D. P. Silva,
• Carolyne B. Braga and
• Roberto Rittner

Beilstein J. Org. Chem. 2017, 13, 925–937, doi:10.3762/bjoc.13.94

• been more widely reported, mainly in gas phase [3][4][5][6][7][8]. Among the 20 amino acids incorporated into proteins, L-methionine (L-Met) and L-cysteine (L-Cys) are the only two containing sulfur. The former is an initiator amino acid in the protein synthesis of all eukaryotics cells [9], whereas

• (NCI) analyses were used. Results and Discussion Esterified derivatives of L-Met and L-Cys The lowest-energy conformers of 1 and 2 and their calculated parameters (ωB97X-D/aug-cc-pVTZ) in gas phase and in solution (IEF−PCM) are shown in the Figure 1 and Table 2, respectively. Each conformer of 1 and 2

• total population of 1, in all different studied media. Although the global minimum of 1 is in the form b in gas phase and also in solution, the three more stable geometries (1-IXb, 1-Xb and 1-XIb) in the former are substituted by three new structures (1-Ib, 1-VIIb and 1-VIIIb) when the solvent is

Continuous-flow processes for the catalytic partial hydrogenation reaction of alkynes

• Carmen Moreno-Marrodan,
• Francesca Liguori and
• Pierluigi Barbaro

Beilstein J. Org. Chem. 2017, 13, 734–754, doi:10.3762/bjoc.13.73

• , which may result in improved selectivity, with no need of additives [76]. Reactor and catalyst design In contrast to unselective processes in the gas phase (e.g., for bulk chemicals production), whose fast interaction with the catalyst may ensure satisfactory conversions under the reaction conditions

• surface and containing precious metal sites (washcoat) [98][99]. They are largely reported in the chemical engineering literature for gas-phase, unselective thermal processes [100][101]. A monolith is “a shaped, fabricated intractable article with a homogeneous microstructure that does not exhibit any

New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

• Pavel Nagorny and
• Zhankui Sun

Beilstein J. Org. Chem. 2016, 12, 2834–2848, doi:10.3762/bjoc.12.283

• (Figure 1) have been utilized to enhance the electrophilicity of organic molecules. Recent spectroscopic and computational studies provided evidence that arenes might form strong hydrogen bonds between aryl C–H groups and anions (Cl−, NO3−, ClO4−, etc.) in the gas phase [28]. In addition, the introduction

• of an electron-withdrawing group into the aryl ring (i.e., NO2, CN, CF3, etc.) could significantly enhance this binding and result in stronger hydrogen bonds between the arene and the anion. Thus, the gas-phase binding energy of the nitrobenzene and chloride anion complex containing two C–H hydrogen

• (calculated) gas phase were further investigated by Huber [89]. Following the aforementioned studies, the Huber group has designed structurally rigid electron-deficient cationic catalysts L22 based on the bis(halobenzimidazolium) scaffold [87]. These catalysts were found to be particularly active, and the

Enzymatic synthesis and phosphorolysis of 4(2)-thioxo- and 6(5)-azapyrimidine nucleosides by E. coli nucleoside phosphorylases

• Vladimir A. Stepchenko,
• Anatoly I. Miroshnikov,
• Frank Seela and
• Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2016, 12, 2588–2601, doi:10.3762/bjoc.12.254

• that natural pyrimidine bases exist in the gas phase and in water solution in the canonical 2,4-diketo form (e.g. [42][43]). The tautomeric structures of 4- and 2-thioanalogues of thymine and uracil have been also investigated by diverse methods and the predominant population of the oxo/thioxo

Combined experimental and theoretical studies of regio- and stereoselectivity in reactions of β-isoxazolyl- and β-imidazolyl enamines with nitrile oxides

• Ilya V. Efimov,
• Marsel Z. Shafikov,
• Nikolai A. Beliaev,
• Natalia N. Volkova,
• Tetyana V. Beryozkina,
• Wim Dehaen,
• Zhijin Fan,
• Viktoria V. Grishko,
• Gert Lubec,
• Pavel A. Slepukhin and
• Vasiliy A. Bakulev

Beilstein J. Org. Chem. 2016, 12, 2390–2401, doi:10.3762/bjoc.12.233

• energies at 298.15 K in gas phase conditions. Structures of the localized transition states. Lengths of the forming bonds are given in Å. Summary of the calculated pathways of the cycloaddition reaction between enamine 1a and benzonitrile oxide 6a. The pathway leading to the observed product is highlighted

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• of the reaction. Interestingly, plotting the data in water (Figure 5) as well as in the gas phase (cf. Supporting Information File 1) for all relevant fragments revealed an exothermic reaction (−6.7 kcal/mol in water) for the hydrolysis of 8a’ (II in Figure 5a) into the protonated fragments (III in

Elongated and substituted triazine-based tricarboxylic acid linkers for MOFs

• Arne Klinkebiel,
• Ole Beyer,
• Barbara Malawko and
• Ulrich Lüning

Beilstein J. Org. Chem. 2016, 12, 2267–2273, doi:10.3762/bjoc.12.219

• carboxylate plane relative to the central six-membered ring is in the same plane in the TATB based MOF PCN-6, the BTB analogue MOF-14 shows a tilt angle of ca. 35°. B3LYP//6-31G* calculations of the isolated linkers in the gas phase result in dihedral angles of 38.5° for BTB and 0.006° for TATB, respectively

Varioloid A, a new indolyl-6,10b-dihydro-5aH-[1]benzofuro[2,3-b]indole derivative from the marine alga-derived endophytic fungus Paecilomyces variotii EN-291

• Peng Zhang,
• Xiao-Ming Li,
• Xin-Xin Mao,
• Attila Mándi,
• Tibor Kurtán and
• Bin-Gui Wang

Beilstein J. Org. Chem. 2016, 12, 2012–2018, doi:10.3762/bjoc.12.188

• order to explore the possibility of axial chirality, torsional angle scans were performed on the lowest-energy M (conformer A) and P (conformer B) helicity gas-phase conformers or atropodiastereomers. Rotational energy barriers between the two isomers were estimated to be ca. 35–42 kJ/mol for TS1 (ωC12

• showed that there is no axial chirality in 1, and equilibrating conformers with M and P helicity are present in solution as obtained in the conformational analysis. The Boltzmann-weighted ECD spectra calculated for both the gas-phase and the solvent model conformers of (2R,3R)-1 at B3LYP/TZVP, BH&HLYP

• ), using dipole-velocity-computed rotational strengths. Boltzmann distributions were estimated from the ZPVE-corrected B3LYP/6-31G(d) energies in the gas-phase calculations and from the B97D/TZVP energies in the PCM model ones. Torsional energy scans and TS calculations were carried out at the B3LYP/6-31G