A combined crystallography and DFT study on ring-shaped Cucurbit[n]urils: structures, surface character, and host-guest recognition

Prediction of binding affinity and enthalpy of CB7 with alkaloids by attach-pull-release molecular dynamics simulations study

Host-guest complex has attracted much attention because of their fantastic capability. Accurate prediction of their binding affinity and enthalpy is essential to the rational design of guest molecules. The attach-pull-release (APR) method proposed by Henriksen et al. (J. Chem. Theory Comput., 2015, 11:4377.) shows good prediction capability of binding affinity especially for host-guest system. In order to further evaluate the performance of APR method in practice, we have conducted the calculations on the macrocycle cucurbit [7]urils (CB7) encapsulated with four structurally similar alkaloids (berberine, coptisine, epiberberine and palmatine) with two force fields (GAFF and GAFF2) and three water models (TIP3P, SPC/E and OPC). Compared to the experimental data, the calculation by the combination of GAFF2 and SPC/E force field presents the best performance, of which the Pearson correlation coefficients (R2) is 0.95, and the root-mean-square-deviation is 3.04 kcal/mol. While the predictions from GAFF force field all overestimated the binding affinity, suggesting a systematic error may be involved. Comparison of calculation also indicates that the accuracy of prediction was susceptible to the combination of force field. Therefore, it would be necessary to repeat the simulation with different combination of force fields in practice.

A theoretical study on the on-off phosphorescence of novel Pt(ii)/Pt(iv)-bisphenylpyridinylmethane complexes

An in-depth theoretical study on the Pt(ii)/Pt(iv)-bisphenylpyridinylmethane complexes was carried out, which focused on the geometric/electronic structures, excitation procedures, on-off phosphorescence mechanisms, and structure-optical performance relationships. The key roles of the linkages (LK) connected in the middle of phenylpyridines were carefully investigated using multiple wavefunction analysis methods, such as non-covalent interaction (NCI) visualizations and natural bond orbital (NBO) studies. The phosphorescence-off phenomenon was considered by hole-electron analysis and visualizations, spin-orbit coupling (SOC) studies, and NBO analysis. Through these investigations, the relationship of the substituents in LK and the optical performances were revealed, as well as the fundamental principles of the phosphorescence-quenching mechanism in Pt(iv) complexes, which pave the way for further performance/structural renovation works. In addition, an intuitive visualization method was developed using a heatmap to quantitatively express the SOC matrix elementary (SOCME), which is helpful for big data simplification for phosphorescence analysis.

Computational exploration for possible reaction pathways, regioselectivity, and influence of substrate in gold-catalyzed cycloaddition of cyanamides with enynamides

The current work focuses on the DFT calculation of the rational mechanism and catalytic activity of the gold(i)-catalyzed isotetradehydro-Diels–Alder cycloaddition of cyanamides and enamides to substituted 2,6-diaminopyridines. IPrAuCl is used as a model catalyst to catalyze cyanamide and enynamide reactants with different substituents in DCM as a research system. DFT data indicates that the catalytic cycle starts from the triple bond coordination between the catalyst's gold cation and the enamide to obtain the gold π-complex, and the cyanamide attacks the alkynyl carbon atom from different directions to generate two reaction channels of five-membered and six-membered heterocycles, respectively. The calculation results show that the 2,6-diaminopyridine compounds produced by this catalytic reaction have lower activation energy and higher reactivity, that is, the pyridine skeleton structure can be easily obtained under mild reaction conditions. At the same time, electron-withdrawing substituents in the reactants are more helpful for the reaction. In addition to being in good agreement with the experimental data, the calculated results also provide an important contribution to the further understanding of the mechanism of such reactions.

The current work focuses on the DFT calculation of the rational mechanism and catalytic activity of the gold(i)-catalyzed isotetradehydro-Diels–Alder cycloaddition of cyanamides and enamides to substituted 2,6-diaminopyridines.