A revised formulation of the generalized subsystem vibrational analysis (GSVA)

In this work, a simplified formulation of our recently developed generalized subsystem vibrational analysis (GSVA) for obtaining intrinsic fragmental vibrations (J Chem Theory Comput 14:2558, 2018) is presented. In contrast to the earlier implementation, which requires the explicit definition of a non-redundant set of internal coordinate parameters to be constructed for the subsystem, the new implementation circumvents this process by employing massless Eckart conditions to the subsystem fragment paired with a Gram-Schmidt orthogonalization to span the same internal vibration space indirectly. This revised version of GSVA (rev-GSVA) can be applied to equilibrium structure as well as transition state structure, and it has been incorporated into the open-source package UniMoVib (https://github.com/zorkzou/UniMoVib).

Supplementary Information

The online version contains supplementary material available at 10.1007/s00214-021-02727-y.

PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids

Visualizing vibrational motions calculated with different ab initio packages requires dedicated post-processing tools. Here, we present a PyMOL plugin called PyVibMS for visualizing the vibrational motions for both molecular and solid systems calculated by mainstream quantum chemical computer programs including Gaussian, Q-Chem, VASP, and CRYSTAL. Benefiting from the continuing development of the PyMOL platform, PyVibMS provides powerful functionalities and user-friendly interface. PyVibMS was written in Python and its open-source nature makes it flexible and sustainable. As an example, the motions of the Konkoli-Cremer local vibrational modes are shown in this work for the first time. PyVibMS is freely available at https://github.com/smutao/PyVibMS . Graphical abstract In this work, a PyMOL plugin named PyVibMS is developed to visualize molecular and lattice vibrations.

Temperature dependence of thermodynamic properties of MoS2 monolayer and single-wall nanotubes: Application of the developed three-body force field

MoS₂ nanostructures, especially mono-, multilayer nanothin films as well as single- and multiwall nanotubes are rather interesting popular objects in nanomaterials chemistry. The thermodynamic properties of inorganic nanotubes, and the temperature dependence of their properties can be efficiently investigated by first-principles and molecular mechanics methods in the framework of harmonic approximation. At the same time, only thin single-wall nanotubes are available for the first-principles calculations. The classical mechanics is suitable to simulate very large atomic systems and their phonon frequencies, but developing sufficiently accurate force field is rather tedious work. Herein, we report the force field fitted to the experimental and first-principles data on the structure of 2H- and 3RMoS₂ polytypes of bulk crystal, structure of monolayer and several bilayers, vibrational frequencies of 2HMoS₂ bulk and monolayer, relative energetic stability of polytypes experimental and first-principles data, elastic constants, strain energy of a (12, 12) MoS₂ nanotube. The thermodynamic functions and their temperature dependence for the armchair and zigzag nanotubes are calculated within the formalism of molecular mechanics using elaborated interatomic potential. The results of molecular mechanics and first-principles method application to the thinnest nanotubes are compared.