Theoretical study on noncovalent interaction of molecular tweezers by Zn(II) salphen-azo-crown ether triads receptor

Experimental and Theoretical Study on Crown Ether-Appended-Fe(III) Porphyrin Complexes and Catalytic Oxidation Cyclohexene with O2

Modifying non-precious metal porphyrins at the meso-position is sufficient to further improve the ability to activate O₂ and the selectivity of the corresponding redox products. In this study, a crown ether-appended Fe(III) porphyrin complex (FeTC₄PCl) was formed by replacing Fe(III) porphyrin (FeTPPCl) at the meso-position. The reactions of FeTPPCl and FeTC₄PCl catalysed by O₂ oxidation of cyclohexene under different conditions were studied, and three main products, 2-cyclohexen-1-ol (1), 2-cyclohexen-1-one (2), and 7-oxabicyclo[4.1.0]heptane (3), were obtained. The effects of reaction temperature, reaction time, and the addition of axial coordination compounds on the reactions were investigated. The conversion of cyclohexene reached 94% at 70 °C after 12 h, and the selectivity toward product 1 was 73%. The geometrical structure optimization, molecular orbital energy level analysis, atomic charge, spin density, and density of orbital states analysis of FeTPPCl, FeTC₄PCl, as well as the oxygenated complexes (Fe-O₂)TCPPCl and (Fe-O₂)TC₄PCl formed after adsorption of O_2, were carried out using the DFT method. The results of thermodynamic quantity variation with reaction temperature and Gibbs free energy variation were also analysed. Finally, based on experimental and theoretical analysis, the mechanism of the cyclohexene oxidation reaction with FeTC₄PCl as a catalyst and O₂ as an oxidant was deduced, and the reaction mechanism was obtained as a free radical chain reaction process.

Independent gradient model based on Hirshfeld partition: A new method for visual study of interactions in chemical systems

The powerful independent gradient model (IGM) method has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we propose an improvement version of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been supported in our wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn). We hope that IGMH will become a new useful method among chemists for exploring interactions in wide variety of chemical systems.

Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies

Matrix metalloproteinase-1 (MMP-1) is a Zn(II) dependent endopeptidase involved in the degradation of collagen, the most abundant structural protein in the extracellular matrix of connective tissues and the human body. Herein we performed a multilevel computational analysis including molecular dynamics (MD), combined quantum mechanics/molecular mechanics (QM/MM), and quantum mechanics (QM) calculations to characterize the structure and geometry of the catalytic Zn(II) within the MMP-1 protein environment in comparison to crystallographic and spectroscopic data. The substrate's removal fine-tuned impact on the conformational dynamics and geometry of the catalytic Zn(II) center was also explored. Finally, the study examined the effect of substituting catalytic Zn(II) by Co(II) on the overall structure and dynamics of the MMP-1 THP complex and specifically on the geometry of the catalytic metal center. Overall our QM/MM and QM studies were in good agreement with the MM description of the Zn(II) centers in the MD simulations.