The determination of point groups from imprecise molecular geometries
This paper by Peter J. Knowles under review took me back forty years when we were working on the symmetry of non-rigid molecules [\textit{E. S. Kryachko} et al., ``Nonrigidity effects of fragments of membrane-active complexons, Int. J. Quantum Chem. 17, 1229--1235 (1980)]. Symmetry is one of the fundamental laws of nature. Symmetry is abundant in physics of many bodies, of molecules in particular. Symmetry has helped scientists to gain insight into the laws of physics, ever since the earliest natural philosophers. To this category refers the present work that proposes a new approach to assign a point group to a molecule when the structure conforms only approximately to the symmetry. Usually, which point-group symmetry must be assigned to a given isolated molecule is trivially straightforward if the coordinates of its atoms are known? Generally speaking, there appear some complicating factors associated with the provenance of the molecular structure. Further, the author discusses the known schemes given in the references [1-24] in determining the approximate molecular symmetry point-group. In contrast, the present work introduces the alternative method that extends and combines the previous approaches and defines measures of broken symmetry based on providing some algorithms, invariant to the coordinate system and supporting the automatic evaluation and assignment of a point-group symmetry, This work also discusses the proper refinement of atomic positions to more precisely satisfy the elements of a chosen point group. Its layout is rather simple and consists of two Sections, 2. Methods and 3. Performance. The former Section is divided into the following Subsections: 2.1. Symmetry measure; 2.2. Optimisation of symmetry operators; 2.3. Choice of coordinate frame: further detail; 2.4. Purification, and 2,5. Software implementation. Section 3 includes Table 1 that illustrates the effect of fully optimising the coordinate frame to minimise the symmetry measure.
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