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

• , whereas by the use of visible light the stretched trans,trans-isomer is formed. By means of quantum chemical calculations and CD spectroscopy we could show that the trans→cis isomerization is spatially directed; that means that one of the two different macrocycles performs a definite clockwise rotation to

• the other, caused by irradiation with UV light. For the cis→trans isomerization counterclockwise rotations are found. Furthermore, quantum chemical calculations reveal that the energy of the cis,cis-isomer is only slightly higher than the energy of the cis,trans-isomer. This effect can be explained by

• -containing macrocycles and the azobenzene bridges having two reactive bromides. The desired container could be isolated in a fair yield taking the multiple reaction pathways into account. Subsequent investigations by means of quantum chemical calculations, UV, CD and NMR spectroscopy revealed that the

Selenophene-containing heterotriacenes by a C–Se coupling/cyclization reaction

• Pierre-Olivier Schwartz,
• Sebastian Förtsch,
• Astrid Vogt,
• Elena Mena-Osteritz and
• Peter Bäuerle

Beilstein J. Org. Chem. 2019, 15, 1379–1393, doi:10.3762/bjoc.15.138

• heterotriacenes 1 and 3 rationalize their unexpected higher melting point compared to 2 and 4. Quantum chemical calculations Quantum chemical DFT and TDDFT calculations (CAMB3LYP and B3LYP with the functional 6-31G++ (d,p)) were performed for the ground and excited state of heterotriacenes 1–4 in order to

• well soluble systems, which allowed for the determination of thermal, optical, and electrochemical properties. By single crystal X-ray structure analysis the geometric structure and packing motifs of selenolotriacenes 2–4 were determined. Quantum chemical calculations allowed for a deeper understanding

• conducted in reflectance mode. During recording the UV–vis–NIR spectra, the applied potential was kept constant. Instrumental artefacts due to the change of the detector were removed and marked in the spectra. Quantum chemical calculations were performed with the Gaussian 09 package: DFT and TDDFT with the

Synthesis of dipolar molecular rotors as linkers for metal-organic frameworks

• Sebastian Hamer,
• Fynn Röhricht,
• Marius Jakoby,
• Ian A. Howard,
• Xianghui Zhang,
• Christian Näther and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1331–1338, doi:10.3762/bjoc.15.132

• be a completely unrealistic endeavour. Here we report on the synthesis of five different dipolar rotors (Figure 2) that are designed to meet the criteria 1–4 listed above, for the use as building blocks in the construction of functional MOFs. Results and Discussion Linker design and quantum chemical

• calculations Aiming at high dipole moments our design was inspired by recent reports of Müllen et al. who reported on very high dipole moments of 1,2-dicyano-4,5-diamino-substituted phenyl derivatives [35]. Unfortunately, amino substituents are not compatible with MOF growth. Cyano substituents could

Phylogenomic analyses and distribution of terpene synthases among Streptomyces

• Lara Martín-Sánchez,
• Kumar Saurabh Singh,
• Mariana Avalos,
• Gilles P. van Wezel,
• Jeroen S. Dickschat and
• Paolina Garbeva

Beilstein J. Org. Chem. 2019, 15, 1181–1193, doi:10.3762/bjoc.15.115

• ionisation of the substrate FPP and the formation of a humulyl cation as an intermediate in the biosynthesis of pentalenene [45][46][48][49], while the later steps of the cyclisation cascade were subject to revision based on the findings of quantum chemical calculations [50][51]. The α-amorphene synthase

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• with a possible character of TICT [55], which could explain a dual-fluorescence and fluorescence quenching in the high polarity media. The charge transfer nature of the transitions for the compounds 8c and 11c, compared to reference compounds 8a and 11a, was confirmed by quantum chemical calculations

• , 46.9, 55.3, 99.5, 101.6, 114.3, 116.2, 123.1, 126.7, 127.3, 146.7, 147.0, 156.6, 156.8, 159.8; HRMS–ESI (m/z): [M + H]+ calcd for C20H22N7O, 376.1880; found, 376.1887. Quantum chemical calculations The initial molecular geometries were generated by using a molecular mechanics method (force field MMF94

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

• . Keywords: binding site; DFT; enzyme mechanism; quantum chemical calculations; ThDP-dependent; Introduction Enzymes that depend on thiamin diphosphate (ThDP, Scheme 1) can be found in a wide range of metabolic pathways. Although they are known to catalyze the formation of C–N, C–O and C–S bonds, ThDP

1,8-Bis(dimethylamino)naphthyl-2-ketimines: Inside vs outside protonation

• A. S. Antonov,
• A. F. Pozharskii,
• P. M. Tolstoy,
• A. Filarowski and
• O. V. Khoroshilova

Beilstein J. Org. Chem. 2018, 14, 2940–2948, doi:10.3762/bjoc.14.273

• ], exists exclusively as a Z-isomer (Figure 2b). Moreover, gas phase quantum chemical calculations show that the E-form is preferable for 5a (ΔE = EZ − EE = 1.66 kcal/mol), 6a (ΔE = 1.19 kcal/mol), and 7a (ΔE = 1.90 kcal/mol), while the Z-form dominates for 4a (ΔE = −2.62 kcal/mol, Figure 3). The

• of the Z-form through formation of a stronger hydrogen bond between the DMSO molecule and the NHb proton [11], which is sterically unhindered and accessible for the solvent. Indeed, X-ray data and quantum chemical calculations show that phenyl and naphthalene rings are almost perpendicular (Figure 2

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• experiments and quantum chemical calculations, the wheels cannot be fully disengaged; however, the wheel–wheel interactions strongly differ for the different oxidation states. The controlled clutching and declutching of 23 by electrochemical stimuli is reminiscent of the operation of a macroscopic friction

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• solution was filtered through a 1.2 µm filter and kept at 4 °C for 12 h. Polymerization was carried out by irradiating the solutions with 254 nm UV light (1 mW/cm2) for 15 min under vigorous stirring in 10 mm quartz cuvettes, placed in a thermostat holder at 25 °C. Quantum chemical calculations Quantum

• chemical calculations were done in several steps: selection of optimal conformers; organization of initial complex geometry; complex optimization procedure. The conformers search procedure has been done only for calix[4]arene’s triazolyl substituents due to complexity of the whole molecule. Conformers of

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

• -docking motifs via the phenyl and vinyl moieties, with an additional less populated OH∙∙∙P(phenyl)-bound isomer detected only by microwave spectroscopy. The correct prediction of the energetic order of the isomers using quantum-chemical calculations turns out to be challenging and succeeds with a

• electronically excited (S1) state is analyzed, in which a destabilization of the OH∙∙∙O structure compared to the S0 state is observed experimentally and theoretically. Keywords: dispersion interactions; IR spectroscopy; quantum-chemical calculations; rotational spectroscopy; structure determination; weak

• Fourier transform microwave (CP-FTMW) spectroscopy. Comparing spectroscopic results with quantum-chemical calculations is often mandatory for the interpretation of experiments. Furthermore, such comparison enables a critical evaluation of the approximations used, comparing the relative stability of

[3 + 2]-Cycloaddition reaction of sydnones with alkynes

• Veronika Hladíková,
• Jiří Váňa and
• Jiří Hanusek

Beilstein J. Org. Chem. 2018, 14, 1317–1348, doi:10.3762/bjoc.14.113

• quantum chemical calculations (DFT/B3LYP-6-31G*) [81] steric effects were identified as the main factor influencing the ratio of both regioisomers. These calculations clearly proved the almost apolar character of both possible transition states giving 3- and 4-BPin substituted pyrazoles through bicyclic

Volatiles from three genome sequenced fungi from the genus Aspergillus

• Jeroen S. Dickschat,
• Ersin Celik and
• Nelson L. Brock

Beilstein J. Org. Chem. 2018, 14, 900–910, doi:10.3762/bjoc.14.77

• product 9 is observed. From A, a second cyclisation event results in D that yields 12 upon deprotonation. Alternatively, A can react by a 1,5-proton shift to E, followed by cyclisation to F and deprotonation to H. This mechanism is favoured by quantum chemical calculations [35] and provides a reasonable

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

• ratiometric fluorescent nature. First, we examined the possible structure and the supramolecular interactions by quantum chemical calculations of our target compound, UHF (uracil-hydroxyflavone) and ATP (see Figure 1 for structures). The theoretical results indicated the possibility of base-pairing

Investigations towards the stereoselective organocatalyzed Michael addition of dimethyl malonate to a racemic nitroalkene: possible route to the 4-methylpregabalin core structure

• Denisa Vargová,
• Rastislav Baran and
• Radovan Šebesta

Beilstein J. Org. Chem. 2018, 14, 553–559, doi:10.3762/bjoc.14.42

• % determined by NMR). Using quantum chemical calculations, we propose approximate transition state models for the stereoselective Michael addition (Figure 2). Geometrical optimizations were performed at HF/6-31G* level and energies were further refined using M06-2X functional with 6-311+G** basis set

• purity of the major diastereomer (er 99:1). With the help of quantum-chemical calculations, we have proposed a transition state model for the Michael addition. Structures of pregabalin and methylpregabalin. Transition state models for the reaction of (R)-6 with dimethyl malonate using catalyst C7 (M06-2X

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

• ° between the donor unit and the nearby phenylene linker for T29 and T30 was confirmed by quantum chemical calculations. Resulting from the almost perfect orthogonality, a good confinement of the electronic density of the two orbitals was obtained with a HOMO level predominantly located on the donor and a

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

• the newly synthesized dyes as DNA fluorogenic binders. A further study of several aspects (including quantum chemical calculations and experimental studies on the DNA binding mechanism) should be carried out on these dyes in order to exploit in details their promising properties. Experimental

Structure–property relationships and third-order nonlinearities in diketopyrrolopyrrole based D–π–A–π–D molecules

• Jan Podlesný,
• Lenka Dokládalová,
• Oldřich Pytela,
• Adam Urbanec,
• Milan Klikar,
• Numan Almonasy,
• Tomáš Mikysek,
• Jaroslav Jedryka,
• Iwan V. Kityk and
• Filip Bureš

Beilstein J. Org. Chem. 2017, 13, 2374–2384, doi:10.3762/bjoc.13.235

• generation. The experimental data were completed by quantum-chemical calculations and structure–property relationships were elucidated. Keywords: calculations; diketopyrrolopyrrole; electrochemistry; electronic spectra; push–pull; third-harmonic generation; Introduction Known for more than 40 years

Conjugated nitrosoalkenes as Michael acceptors in carbon–carbon bond forming reactions: a review and perspective

• Yaroslav D. Boyko,
• Valentin S. Dorokhov,
• Alexey Yu. Sukhorukov and
• Sema L. Ioffe

Beilstein J. Org. Chem. 2017, 13, 2214–2234, doi:10.3762/bjoc.13.220

• phosphinyl nitrosoalkenes NSA15 (derived from the corresponding α-bromooximes) with electron-rich nitrogen heterocycles to give adducts 69 is described and the comparison of electrophilic aromatic substitution (1) and cycloaddition (2) routes is discussed [59] (Scheme 24). Quantum-chemical calculations

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

• paraquat (7) in solution is well correlated with the data for these complexes in the crystalline state revealed by quantum chemical calculations [41] except complexes with paraquat derivative 10 (Table 4). The calculated data show that the main contribution to the stabilization of the complexes in the

• with clips 1–6. Complex stability constants of molecular clips 1–5 with guests 7–10 in acetonitrile at 20 °C. Contribution of polyether oxygen atoms of molecular clips 1–5 to the binding of paraquat. The host–guest interaction energies are estimated by quantum chemical calculations (b97-D3/def2-tzvp

• (Figure 7). Within the row molecules are arranged by π–π stacking interactions between the side aromatic fragments of the clips with a centroid–centroid distance in the range of 3.51–3.71 Å. There are acetonitrile solvate molecules and hexafluorophosphate anions between neighboring rows. Quantum chemical

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

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

• analysis; cysteine; methionine; NMR spectroscopy; quantum chemical calculations; Introduction Amino acids constitute the building blocks of proteins and peptides, which play an important role in numerous biological processes [1][2]. However, their studies in both isolated and condensed phases have been

• quantum chemical calculations [16][17][18][19]. In spite of these many studies performed, there is still a lack of information about the effects that rule their conformational isomerism. Additionally, the conformational flexibility of both amino acids leads to a variety of low energy geometries, which

• insights about the main conformers and the operating effects in the compounds, both in isolated phase and in various aprotic solvents, 1H NMR spectroscopy and quantum chemical calculations, including natural bond orbitals (NBO), quantum theory of atoms in molecules (QTAIM), and noncovalent interactions

Metal-free hydroarylation of the side chain carbon–carbon double bond of 5-(2-arylethenyl)-3-aryl-1,2,4-oxadiazoles in triflic acid

• Anna S. Zalivatskaya,
• Dmitry S. Ryabukhin,
• Marina V. Tarasenko,
• Alexander Yu. Ivanov,
• Irina A. Boyarskaya,
• Elena V. Grinenko,
• Ludmila V. Osetrova,
• Eugeniy R. Kofanov and
• Aleksander V. Vasilyev

Beilstein J. Org. Chem. 2017, 13, 883–894, doi:10.3762/bjoc.13.89

• nitrogen may be protonated depending on the substituents attached to the heterocyclic system [50]. To investigate this issue in more detail we undertook a theoretical study on the protonation of 5-(2-phenylethenyl)-3-phenyl-1,2,4-oxadiazole (1a) by quantum-chemical calculations. Table 1 contains data

Synthesis and optical properties of new 5'-aryl-substituted 2,5-bis(3-decyl-2,2'-bithiophen-5-yl)-1,3,4-oxadiazoles

• Anastasia S. Kostyuchenko,
• Tatyana Yu. Zheleznova,
• Anton J. Stasyuk,
• Aleksandra Kurowska,
• Wojciech Domagala,
• Adam Pron and
• Alexander S. Fisyuk

Beilstein J. Org. Chem. 2017, 13, 313–322, doi:10.3762/bjoc.13.34

• induce non-planarity due to steric hindrance, which lowers the effective conjugation. This problem will be discussed in detail in the section devoted to quantum chemical calculations. When excited by UV light, all studied compounds emit blue (468, 473 nm) or bluish-green (499, 501) light (Table 2

• observed in D–A–D-type conjugated molecules [28]. DFT calculations To gain a deeper understanding of the electronic and photophysical properties of the synthesized 5'-aryl-substituted 2,5-bis(3-decyl-2,2'-bithiophen-5-yl)-1,3,4-oxadiazoles we have performed quantum-chemical calculations for four

Regiochemistry of cyclocondensation reactions in the synthesis of polyazaheterocycles

• Patrick T. Campos,
• Leticia V. Rodrigues,
• Andrei L. Belladona,
• Caroline R. Bender,
• Juliana S. Bitencurt,
• Fernanda A. Rosa,
• Davi F. Back,
• Helio G. Bonacorso,
• Nilo Zanatta,
• Clarissa P. Frizzo and
• Marcos A. P. Martins

Beilstein J. Org. Chem. 2017, 13, 257–266, doi:10.3762/bjoc.13.29

• quantum-chemical calculations were used to understand the regiochemistry of the obtained products. Results and Discussion β-Enaminodiketone 1, which is a key precursor for the synthesis of polyazaheterocyclic compounds, was synthesized by methods previously described by our research group [17][18][19][20

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

• a Wittig salt with a longer alkyl chain the synthesis of the fatty acid 11d with a chain of 21 carbon atoms in addition to the BTD unit was equally feasible. Spectroscopic properties and quantum chemical calculations If one follows the oligoene chain and includes the two s-cis-shaped double bonds of