Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• the DFT calculation realized by the PWscf code of Quantum ESPRESSO [30][31][32], the DFT-D3 correlation [33] together with PBEsol functional [34] for the exchange-correlation functional described van der Waals interaction between graphene and pyrene fragment in PASE. Ultrasoft pseudopotentials [35

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• calculations. The fullerene dimerization mechanism inside a SWCNT was also studied by density functional theory applied to periodic systems through VASP code [31]. The exchange-correlation functional used was PBE with the zero damping DFT-D3 method of Grimme et al. [16]. Inner electrons were replaced by PAW

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

• 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

• method chosen (DFT-D3) since a scan with a second method (DFT-TS) leads to the same picture with only slight numeric differences (Figure S2, Supporting Information File 1). The double-adsorption structure 3 will now lead to a blocking of two dimers and thus result on average in a distance of two dimers

• a clean and precovered Si(001) surface. All values in kJ·mol−1. Supporting Information The supporting information shows PES scans comparing DFT-D3 and DFT-TS, scans at different adsorption heights as well as Cartesian coordinates and total energies for the equilibrium structures presented

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

• -corrected density functional theory (DFT-D3) [44][45], spin-component-scaled approximated coupled cluster-singles-doubles (SCS-CC2) [46] as well as explicitly correlated local coupled cluster theory (LCCSD(T0)-F12) [47] calculations, the latter allowing for a quantification and visualization of London

• 36885 cm−1 containing an OH stretching vibration of a PVE–MeOH dimer. Comparing the calculated OH stretching frequencies for the different isomers obtained at the DFT-D3 and SCS-CC2 levels (cf. Table 1) to the experiment does not allow for a clear structural assignment: the DFT-D3 calculations show the

• analysis on a molecular complex with a very delicate balance between, for the first time, three different binding motifs. This provides an excellent benchmark system for theory, since DFT-D3 as well as SCS-CC2 methods fail in predicting the correct energetic order, whereas LCCSD(T0)-F12 succeeds in the

Cycloheximide congeners produced by Streptomyces sp. SC0581 and photoinduced interconversion between (E)- and (Z)-2,3-dehydroanhydrocycloheximides

• Li Yang,
• Ping Wu,
• Jinghua Xue,
• Huitong Tan,
• Zheng Zhang and
• Xiaoyi Wei

Beilstein J. Org. Chem. 2017, 13, 1039–1049, doi:10.3762/bjoc.13.103

• carried out on two possible stereoisomers, (4R,6R,αS)-1 and (4R,6R,αR)-1. MMFF conformational search and subsequent geometry optimization using the DFT-D3 method at the B3LYP-D3/6-31G(d) level followed by a higher level of energy calculations at the B3LYP-D3/def2-TZVP level afforded 14 and 11 distinctive

• functional theory (TDDFT) calculations were performed with the Gaussian 09 program package [24]. For computations of ECD spectra, the conformers generated by a MMFF conformational search in an energy window of 10 kcal/mol were subjected to geometry optimization using the dispersion-corrected DFT-D3 method

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

• adsorption of aromatic compounds. In the last years much effort has been directed to the development of DFT methods that eliminate this shortage [13][14][15][16][17][18][19][20][21][22][23][24]. One of them is a damped empirical correction called DFT-D3 which was proposed by Grimme et al. for molecular

• 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

• only in the damping function for short range interaction. Due to the computational efficiency of the D3 correction schemes it is possible to perform DFT-D3 calculations with nearly the same computational effort as standard DFT calculations. Only the calculation of three-body terms can become expensive

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

• substitution with different functional groups and of molecular flexibility by changing within the axle from a single C–C bond to a double C=C bond. Therefore, we present static quantum chemical calculations at the dispersion-corrected density functional level (DFT-D3) for several Leigh-type rotaxanes. The

• less than 2%. However, care has to be taken when comparing results calculated in the gas phase with those obtained in the condensed phase due to non-local crystal packing effects. The computed DFT-D3 formation energies of the non-covalently bound rotaxanes in the gas phase range from about −41 to −58

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

• indanes or dihydrobenzofurans are too slow to be useful synthetically. Keywords: aromatic substitution; computational chemistry; DFT-D3; free radical; polar effects; radical reaction; Introduction The development of efficient catalytic reactions is one of the central issues of chemistry [1][2]. Radical

• 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

• with DFT-D3 (termed PW6B95-D3 from now on) is the most robust and accurate general purpose hybrid functional and is therefore used also in this work. As a meta-hybrid functional it partially avoids the SIE by admixture of non-local Fock-exchange (28%) leading to reasonable reaction barriers [27] which