Complexes of resorcin[4]arene with secondary amines: synthesis, solvent influence on “in-out” structure, and theoretical calculations of non-covalent interactions

• Waldemar Iwanek

Beilstein J. Org. Chem. 2023, 19, 1525–1536, doi:10.3762/bjoc.19.109

• r2scan-3c/CPCM functional in an appropriate solvent was applied to the 15 complexes with the lowest energy. The geometry of the lowest energy complex was then reoptimized using the PBE0 functional [24], the D4 dispersion correction [25], the def2-mTZVPP functional basis [21], and the CPCM solvent model

• complexes were refined using the PBE0 functional with D4 dispersion correction and the CPCM solvent model (ORCA5.0.3). HFLD calculations with the def2-TZVP(-f) basis and the SMD solvent model were performed using the ORCA5.03 program with RIJCOSX approach [31] and NormalPNO settings. The acidity of hydroxy

Asymmetric tandem conjugate addition and reaction with carbocations on acylimidazole Michael acceptors

• Brigita Mudráková,
• Renata Marcia de Figueiredo,
• Jean-Marc Campagne and
• Radovan Šebesta

Beilstein J. Org. Chem. 2023, 19, 881–888, doi:10.3762/bjoc.19.65

• ). Single point energy calculations were performed using long-range corrected hybrid density functional ωB97X, which offer very good performance and have been recommended for general use in chemistry [27] with empirical dispersion correction D4 [28] (ωB97X-D4) and the triple-zeta def2-TZVPPD basis set [29

Eschenmoser coupling reactions starting from primary thioamides. When do they work and when not?

• Lukáš Marek,
• Jiří Váňa,
• Jan Svoboda and
• Jiří Hanusek

Beilstein J. Org. Chem. 2023, 19, 808–819, doi:10.3762/bjoc.19.61

• functional with D3 Grimme’s dispersion correction [42][43] and 6-311++G(d,p) basis set. All reported minima and transition state structures were confirmed by calculation and diagonalization of their Hessian matrices. The reported energies are Gibbs free energies calculated with the SMD method in N,N

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• as a control) using M11-L optimization. Two fourth rung [90] functionals, M11 and MN12-SX [105][106], also failed to give any improvement (Table 4, entries 19 and 20), and these were also worse than the older fourth rung [90] functional M06-2X. Grimme’s D3 dispersion correction has been recommended

• corrected range-separated functional with dispersion correction [96], was also found to be highly accurate, and it was the most recently developed of the five representative functionals chosen by Jensen for evaluation [8]. Somewhat surprisingly, given the long-range correction that we previously found had

Electron-rich triarylphosphines as nucleophilic catalysts for oxa-Michael reactions

• Susanne M. Fischer,
• Simon Renner,
• A. Daniel Boese and
• Christian Slugovc

Beilstein J. Org. Chem. 2021, 17, 1689–1697, doi:10.3762/bjoc.17.117

• TURBOMOLE program (version 7.4.1) [43]. Geometries were pre-optimized using the PBE [44] functional, the def2-SVPD [45][46] basis set and D3 [47] dispersion correction. All structures were then re-optimized using the hybrid functional B3LYP [48][49][50][51] D3 with the def2-TZVPPD basis set. For gas-phase

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• calculations were performed on a simplified model to provisionally validate this proposed mechanism. The geometry of the intermediate species were optimized with Gaussian 09 software [44], using the B3LYP/LANL2DZ theory level for Zr and B3LYP/6-31G(d,p) for other atoms, with GD3 empirical dispersion correction

Fluorine effect in nucleophilic fluorination at C4 of 1,6-anhydro-2,3-dideoxy-2,3-difluoro-β-D-hexopyranose

• Danny Lainé,
• Vincent Denavit,
• Olivier Lessard,
• Laurie Carrier,
• Charles-Émile Fecteau,
• Paul A. Johnson and
• Denis Giguère

Beilstein J. Org. Chem. 2020, 16, 2880–2887, doi:10.3762/bjoc.16.237

• , DFT calculations were performed with Gaussian 09, revision E.01 [44] to evaluate the hypothesis for the formation of oxiranium ion A. Calculations were performed with the CAM-B3LYP functional [45][46][47] using Grimme’s D3 dispersion correction [48] and the 6-31+G(d,p) basis set. The results of our

A combinatorial approach to improving the performance of azoarene photoswitches

• Joaquin Calbo,
• Aditya R. Thawani,
• Rosina S. L. Gibson,
• Andrew J. P. White and
• Matthew J. Fuchter

Beilstein J. Org. Chem. 2019, 15, 2753–2764, doi:10.3762/bjoc.15.266

• the possible conformers both in the Z- and E-forms were fully optimized by using the hybrid exchange-correlation PBE0 functional [37] including the Grimme’s dispersion correction in its latest version (D3) [38]. The split-valence Pople’s basis set 6-31G** was used throughout [39]. Transition states

Anion-driven encapsulation of cationic guests inside pyridine[4]arene dimers

• Anniina Kiesilä,
• Jani O. Moilanen,
• Anneli Kruve,
• Christoph A. Schalley,
• Perdita Barran and
• Elina Kalenius

Beilstein J. Org. Chem. 2019, 15, 2486–2492, doi:10.3762/bjoc.15.241

• ) without (PBE0/def2-TZVP) and with (PBE0-D3/def2-TZVP) dispersion correction because in the gas phase dispersion plays an important role in the formation of supramolecular complexes [24][25][26][27][28][29][30]. Conformational analysis was first performed for both tautomers of the monomer to ensure that

• dispersion correction (hydrogen bond lengths are listed in Table S2, Supporting Information File 1). This is expected, because the standard hybrid functionals are able to describe strong hydrogen bonds such as NH···O and OH···O in a reasonable manner [31][32]. Due to the encapsulated guest molecule, the [12

• File 1). When the dispersion correction and/or the counterion(s) are taken into account, the energy analysis supports the findings obtained from ESI-MS studies, geometry optimizations and ESP surfaces: The Me4N+ cation is most likely bound inside the cavity of 12. It is also important to note that the

Fluorinated azobenzenes as supramolecular halogen-bonding building blocks

• Esther Nieland,
• Oliver Weingart and
• Bernd M. Schmidt

Beilstein J. Org. Chem. 2019, 15, 2013–2019, doi:10.3762/bjoc.15.197

• dispersion correction, using the Gaussian 16 program package (see Supporting Information File 1). The azobenzenes were embedded in a continuum using the polarizable continuum model (PCM) for the solvent MeCN. The DGZVP all electron basis was used for iodine. Vertical excitation energies for the π→π* and n→π

• OriginPro. Kinetic measurements were performed in MeCN at 60 °C (Supporting Information File 1). Activation process parameters for the E→Z isomerisation in MeCN at 60 °C, B3LYP, def-TZVP basis for C, H, N, F, DGZVP all electron basis for iodine. Grimme D3 dispersion correction was applied. Values were

Transient and intermediate carbocations in ruthenium tetroxide oxidation of saturated rings

• Manuel Pedrón,
• Laura Legnani,
• Maria-Assunta Chiacchio,
• Pierluigi Caramella,
• Tomás Tejero and
• Pedro Merino

Beilstein J. Org. Chem. 2019, 15, 1552–1562, doi:10.3762/bjoc.15.158

• ]. Computations were done using the B3LYP functional [48][49] in conjunction with Grimme’s dispersion correction [50][51] (henceforth referred to as B3LYP-d3bj). The standard basis set Def2SVP was employed [52][53]. For the purpose of comparison optimizations at gas phase and considering solvent effects (both

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

• potentials B3LYP [53][54][55] and B3LYP-D3 [56][57]. The latter includes an additional dispersion correction and describes dispersion interactions more accurately for larger atomic distances. As basis set 6-31G* [58][59] was applied. In the case of the cis,trans- and cis,cis-isomers we tried to calculate all

• required. This is ca. 4 kcal/mol more than twice the energy of the trans→cis isomerization of azobenzene. Accordingly, the cis,cis-10 exhibits an additional strain energy of about 4 kcal/mol compared to trans,trans-10. A completely different picture emerges when the dispersion correction D3 is taken into

Adhesion, forces and the stability of interfaces

• Robin Guttmann,
• Johannes Hoja,
• Christoph Lechner,
• Reinhard J. Maurer and
• Alexander F. Sax

Beilstein J. Org. Chem. 2019, 15, 106–129, doi:10.3762/bjoc.15.12

• not this assumption is justified depends on the many-body system, and on the extent to which the interaction between the real particles is included in the quasi-particles. Many dispersion-correction strategies assume pair-wise additivity of the long-range electron correlation energy. The properties of

• the quasi-atoms may be obtained by fitting them to interaction energies calculated with other high-level methods. This strategy is used, for example, in Grimme’s D2 method [27], for the calculation of the dispersion energy in the dlDF+D method by Szalewicz [28][29], and for the dispersion correction

The influence of the cationic carbenes on the initiation kinetics of ruthenium-based metathesis catalysts; a DFT study

• Magdalena Jawiczuk,
• Angelika Janaszkiewicz and
• Bartosz Trzaskowski

Beilstein J. Org. Chem. 2018, 14, 2872–2880, doi:10.3762/bjoc.14.266

• method equal to 20.4 kcal/mol, in perfect agreement with the experimental value of 19.88 kcal/mol [21]. The addition of the D3 dispersion correction increases this value to 29.2 kcal/mol. For the carbodicarbene catalyst the experimental value is 23.5 kcal/mol [48] and we found the value of 23.9 kcal/mol

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 PBE functional [16][17], the DFT-D3 dispersion correction [18][19] and the PAW formalism [20][21] with a basis set cutoff of Ecutoff = 400 eV. Electronic k space was sampled using a Γ(221) grid. Some calculations used the DFT-TS scheme for comparison [22]. Self-consistent field (SCF) and

• Figure 5b. Now, significant differences can be found between the PES scan with (top panels) and without (bottom panels) considering dispersion effects. For the computations without dispersion correction, the PES is again rather featureless and the interaction between adsorbate and surface is very weak

Calixazulenes: azulene-based calixarene analogues – an overview and recent supramolecular complexation studies

• Paris E. Georghiou,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Hidetaka Nishimura,
• Jaehyun Lee,
• Atsushi Wakamiya and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2018, 14, 2488–2494, doi:10.3762/bjoc.14.225

• with the empirical dispersion correction was used with the standard 6-31G(d) basis set [26]. We had previously described the use of this system in our previous studies in particular, in reference [20] as being more reliable than the use of B3LYP/6-31G(d) with our systems. Furthermore, for the halide

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

• reaction additionally with B3LYP without dispersion correction and the dispersion-corrected M06-L functional under otherwise identical conditions as a first starting point. Independent of the computational method, the overall reaction free energy for the transformation of Scheme 2 is almost identical

• the Supporting Information File 1 for details) resulted in a comparable profile to that obtained with B3LYP-D3BJ (black lines in Figure 1), a significant deviation was observed when the latter was used without any dispersion correction (red lines in Figure 1). All cobalt complexes are substantially

• numerical quadrature grid in the gas phase. The hybrid functional B3LYP [53][54] with and without Grimme’s dispersion correction D3 (Becke–Johnson damping) [35][36] as well as Truhlar’s dispersion-corrected M06-L [55] functional were employed in this investigation. For the latter, the density fitting RI-J

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

• with D3(BJ) dispersion correction, as well as the close H–H contacts in all compounds of about 2.4 Å to 3.0 Å support the stabilizing effect of LD interactions in (Z)-azobenzenes 4–7. Figure 1 visualizes the computational findings for the compared conformers of (Z)-4. A noncovalent interaction (NCI

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

• a dispersion correction. The latest variants of these approaches have been highly successful in predicting key properties of a wide range of molecules and materials, such as binding energies and molecular/material structures [4][5][15]. Methods are increasingly converging towards accurate prediction

• of dispersion correction models. Note, this is different to seamless approaches like MP2, RPA or other quantum chemistry methods which include dispersion forces automatically. Common van der Waals corrections can be broadly divided into three categories, as will be detailed below. Substantial effort

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

• correction [50][51] and the 6-31G basis set [52]. Subsequently, the geometries obtained were utilized for generating the initial structures of the complexes, which were optimized with the same functional and basis set. To mimic the experimental conditions all the DFT calculations were performed using the

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

• , Figures S11–S14). Computational details. Calculations were carried out using the B3LYP hybrid functional combined with an empirical Grimme’s D3 dispersion correction [55] (B3LYP-D3) implemented in Gaussian 09 [56]. The standard 6-311+G(2d,p) basis set with the ultrafine method was used for C, H, N, F, Cl

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