ChemShell is a modular computational chemistry package with a particular focus on hybrid quantum mechanical/molecular mechanical (QM/MM) simulations. A core set of chemical data handling modules and scripted interfaces to a large number of quantum chemistry and molecular modeling packages underpin a flexible QM/MM scheme. ChemShell has been used in the study of small molecules, molecular crystals, biological macromolecules such as enzymes, framework materials including zeolites, ionic solids, and surfaces. We outline the range of QM/MM coupling schemes and supporting functions for system setup, geometry optimization, and transition‐state location (including those from the open‐source DL‐FIND optimization library). We discuss recently implemented features allowing a more efficient treatment of long range electrostatic interactions, X‐ray based quantum refinement of crystal structures, free energy methods, and excited‐state calculations. ChemShell has been ported to a range of parallel computers and we describe a number of options including parallel execution based on the message‐passing capabilities of the interfaced packages and task‐farming for applications in which a number of individual QM, MM, or QM/MM calculations can performed simultaneously. We exemplify each of the features by brief reference to published applications.This article is categorized under: Software > Quantum Chemistry Software > Molecular Modeling

The layered semiconductor SnSe is one of the highest-performing thermoelectric materials known. We demonstrate, through a first-principles lattice-dynamics study, that the high-temperature $Cmcm$ phase is a dynamic average over lower-symmetry minima separated by very small energetic barriers. Compared to the low-temperature $Pnma$ phase, the $Cmcm$ phase displays a phonon softening and enhanced three-phonon scattering, leading to an anharmonic damping of the low-frequency modes and hence the thermal transport. We develop a renormalization scheme to quantify the effect of the soft modes on the calculated properties, and confirm that the anharmonicity is an inherent feature of the $Cmcm$ phase. These results suggest a design concept for thermal insulators and thermoelectric materials, based on displacive instabilities, and highlight the power of lattice-dynamics calculations for materials characterization.

The concepts of oxidation state and atomic charge are entangled in modern materials science. We distinguish between these quantities and consider their fundamental limitations and utility for understanding material properties. We discuss the nature of bonding between atoms and the techniques that have been developed for partitioning electron density. While formal oxidation states help us count electrons (in ions, bonds, lone pairs), variously defined atomic charges are usefully employed in the description of physical processes including dielectric response and electronic spectroscopies. Such partial charges are introduced as quantitative measures in simple mechanistic models of a more complex reality, and therefore may not be comparable or transferable. In contrast, oxidation states are defined to be universal, with deviations constituting exciting challenges as evidenced in mixed-valence compounds, electrides and highly correlated systems. This Perspective covers how these concepts have evolved in recent years, our current understanding and their significance.

We review the growing role of computational techniques in modelling the structures and properties of nano-particulate oxides and sulphides. We describe the main methods employed, including those based on both electronic structure and interatomic potential approaches. Particular attention is paid to the techniques used in searching for global minima in the energy landscape defined by the nano-particle cluster. We summarise applications to the widely studied ZnO and ZnS systems, to silica nanochemistry and to group IV oxides including TiO₂. We also consider the special case of silica cluster chemistry in solution and its importance in understanding the hydrothermal synthesis of microporous materials. The work summarised, together with related experimental studies, demonstrates a rich and varied nano-cluster chemistry for these materials.