Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

4 years ago

Rhorix: An interface between quantum chemical topology and the 3D graphics program blender

Kenneth L. Sale, Blake A. Simmons, Paul L. A. Popelier, Matthew J. L. Mills

Chemical research is assisted by the creation of visual representations that map concepts (such as atoms and bonds) to 3D objects. These concepts are rooted in chemical theory that predates routine solution of the Schrödinger equation for systems of interesting size. The method of Quantum Chemical Topology (QCT) provides an alternative, parameter-free means to understand chemical phenomena directly from quantum mechanical principles. Representation of the topological elements of QCT has lagged behind the best tools available. Here, we describe a general abstraction (and corresponding file format) that permits the definition of mappings between topological objects and their 3D representations. Possible mappings are discussed and a canonical example is suggested, which has been implemented as a Python “Add-On” named Rhorix for the state-of-the-art 3D modeling program Blender. This allows chemists to use modern drawing tools and artists to access QCT data in a familiar context. A number of examples are discussed. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. Rhorix, a Blender Python Add-On for rendering of quantum chemical topologies, is introduced and its implementation and several applications are discussed in detail. The program allows high-quality visual representation of chemical concepts in terms of their underlying quantum mechanics. This image shows the topology of hexamethylenetetramine, the first experimentally-determined molecular structure of a carbon compound. Every type of common critical point is present, and the cage structure is highlighted by light emanating from its center.

Publisher URL: http://onlinelibrary.wiley.com/resolve/doi

DOI: 10.1002/jcc.25054