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

• at the B3LYP/Def2-TZVP level of theory combined with D3BJ dispersion correction. The reactions of benzonitrile oxide with both E- and Z-imidazolyl enamines have been shown to proceed stereoselectively to form trans- and cis-isoxazolines, respectively. The preference of E-isomers over Z-isomers

• ][40][41][42] theory level. Grimme’s D3BJ dispersion correction [43][44] was applied to improve the long range interactions related calculation accuracy [45]. To the best of our knowledge there is not a high level of theoretical investigations reported on the possible reaction pathways of nitrile

Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin

• Waratchada Sangpheak,
• Jintawee Kicuntod,
• Roswitha Schuster,
• Thanyada Rungrotmongkol,
• Peter Wolschann,
• Nawee Kungwan,
• Helmut Viernstein,
• Monika Mueller and
• Piamsook Pongsawasdi

Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297

• for analysis. The MM- and QM-PBSA/GBSA calculations were conducted to estimate the binding free energy of the inclusion complex [40][60]. For QM calculation, the single point M06-2X/6-31+G** level of theory including the empirical dispersion correction energy [46] was treated on the same set of

Why base-catalyzed isomerization of N-propargyl amides yields mostly allenamides rather than ynamides

• Armando Navarro-Vázquez

Beilstein J. Org. Chem. 2015, 11, 1441–1446, doi:10.3762/bjoc.11.156

• . From the ωB97 family we tested the ωB97 form, the ωB97X, which includes exact short-range HF exchange, and in addition the ωB97XD functional, which also includes Grimme’s dispersion correction [16]. The DFT tests employed a medium-size 6-31+G** basis in search of a methodology applicable to relatively

First principle investigation of the linker length effects on the thermodynamics of divalent pseudorotaxanes

• Andreas J. Achazi,
• Doreen Mollenhauer and
• Beate Paulus

Beilstein J. Org. Chem. 2015, 11, 687–692, doi:10.3762/bjoc.11.78

• linker shows an enhanced binding strength due to electronic effects, namely the dispersion interaction between the linkers from the guest and the host. For the longer linkers this ideal packing is not possible due to steric hindrance. Keywords: density functional theory (DFT); dispersion correction

• (deviation less than 0.3%). This very good agreement is somewhat fortunate, because a basis set extrapolation with DZ and TZ is only accurate to within a few percent. Additionally, the possible errors of the functional and the dispersion correction can also be in the range of 10% for the system under

• investigation. A more detailed analysis of the accuracy of the TPSS-D3(BJ) functional has been performed for the crown-6/ammonium complex in [25]. Another point to remark is that even for the monovalent system about 36% of the electronic interaction energy is due to the dispersion correction. 2) The finite

Theoretical study of the adsorption of benzene on coinage metals

• Werner Reckien,
• Melanie Eggers and
• Thomas Bredow

Beilstein J. Org. Chem. 2014, 10, 1775–1784, doi:10.3762/bjoc.10.185

• = Cu), silver (M = Ag) and gold (M = Au) is studied on the basis of density functional theory (DFT) calculations with an empirical dispersion correction (D3). Variants of the Perdew–Burke–Ernzerhof functionals (PBE, RPBE and RevPBE) in combination with different versions of the dispersion correction

• ; dispersion correction; template; Introduction The adsorption of organic molecules on metals is of great interest since the formation of thin films and self-assembled monolayers opens the way toward a functionalization of surfaces [1][2][3][4][5][6][7][8]. The adsorbed molecules often contain an aromatic

• systems [13]. The D3-dispersion correction to the DFT energy is calculated by summation over pair potentials. Non-additive effects of dispersion interaction can be treated on the basis of three-body terms D3(ABC) [13]. The most recent DFT-D3(BJ) method [16] differs from the original DFT-D3 essentially

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• identity technique (RI) and the def2-TZVP basis set were applied [33][34] together with the dispersion correction D3 [35][36]. This level of theory is abbreviated as TPSS-D3/def2-TZVP. All molecular calculations were performed by using the TURBOMOLE 6.4 program package [33]. The convergence criterion for

• missing non-local correlation interactions through the atom-pairwise London dispersion correction D3 in the Becke–Johnson damping scheme [35][36]. A single (isolated) dimer was optimized with the same technical setup in a large unit cell with minimum intermolecular atom-atom distance of 16 Å. This method

Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

• Andreas Gansäuer,
• Meriam Seddiqzai,
• Tobias Dahmen,
• Rebecca Sure and
• Stefan Grimme

Beilstein J. Org. Chem. 2013, 9, 1620–1629, doi:10.3762/bjoc.9.185

• problems, e.g., self-interaction error (SIE) leading to underestimated reaction barriers and the lack of long-range electron correlation (London dispersion) effects. Regarding the latter problem, one of the most successful and widely used dispersion correction schemes is DFT-D3, in which a damped, atom

• applied. The numerical quadrature grid m4 was employed for integration of the exchange-correlation contribution. For all geometry optimizations as well as single-point calculations the D3 dispersion correction scheme [26] applying Becke–Johnson (BJ) damping [48][49][50] was used. Computations of the

• the D3 correction is used and highly overestimates the barrier (by about 3 kcal mol−1) without the D3 correction. The plain PW6B95 functional without the dispersion correction still overestimates the barrier by 0.7 kcal mol−1. However, the use of PW6B95-D3 provided an energy of activation that differs

A computational study of base-catalyzed reactions of cyclic 1,2-diones: cyclobutane-1,2-dione

• Nargis Sultana and
• Walter M. F. Fabian

Beilstein J. Org. Chem. 2013, 9, 594–601, doi:10.3762/bjoc.9.64

• trends agree very well with that obtained with CEPA/1 [Supporting Information File 1; the corresponding correlation coefficients R2 are 0.992 (M06-2X); 0.997 (MP2 and SCS-MP2); and 0.999 (EC)]. Inclusion of an empirical dispersion correction (DFTD3 [28]) in the M06-2X results further lowers the relative

A new intermediate in the Prins reaction

• Shinichi Yamabe,
• Takeshi Fukuda and
• Shoko Yamazaki

Beilstein J. Org. Chem. 2013, 9, 476–485, doi:10.3762/bjoc.9.51

• dispersion correction method (ωB97XD [29]) were applied to the rate-determining step of the propene reaction TS1(Me). The basis sets employed were 6-31G(d) and 6-311+G(d,p). Transition states (TSs) were sought first by partial optimizations at bond interchange regions. Second, by the use of Hessian matrices