There are various nonplanar heteroatom analogues of benzene—cyclic 6π electron systems—and among them, hexasilabenzene (Si6H6) is well known as a typical example. To determine the factors that control their planarity, quantum chemical calculations and an energy component analysis were performed. The results show that the energy components mainly controlling the planarity of benzene and hexasilabenzene are different. For hexasilabenzene, electron repulsion energy was found to be significantly important for the planarity. The application of the pseudo Jahn–Teller effect and the Carter–Goddard–Malrieu–Trinquier model for the interpretation of the planarity of the benzene analogues was also investigated. Furthermore, based on the quantitative results, it was revealed that the planarization of hexasilabenzene is realized by introducing substituents with π‐accepting ability, such as the boryl group, that bring about a reduction of the π‐electron repulsion on the silicon skeleton. © 2018 Wiley Periodicals, Inc.

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A fast quantum-mechanical approach, density-functional tight-binding combined with the fragment molecular orbital method and periodic boundary conditions, is used to optimize atomic coordinates and cell parameters for a set of protein crystals: 1ETL, 5OQZ, 3Q8J, 1CBN, and 2VB1. Good agreement between experimental and calculated structures is obtained for both atomic coordinates and cell parameters. Sterical clashes present in the experimental structures are corrected by simulations. The partition analysis is extended to treat periodic boundary conditions and applied to analyze protein−solvent interactions in crystals.

A decomposition of the free energy is developed in the many-body expansion framework of the fragment molecular orbital (FMO) method combined with umbrella sampling molecular dynamics (MD). In FMO/MD simulations, performed with density-functional tight-binding and periodic boundary conditions, all atoms are treated quantum mechanically. The free energy is computed and decomposed for a series of SN2 Menshutkin reactions in water. The barrier lowering by the solvent is attributed to the competition between the solvent polarization and the solute–solvent interactions including charge transfer.