Near-symmetry in molecular structures can be rigorously converted to exact symmetry using continuous symmetry measures.
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Peer-reviewed literature on continuous symmetry measures demonstrates that software implementations can calculate the coordinates of the nearest symmetric structure, allowing near-symmetry to be quantitatively converted to exact symmetry.
The structure of molecular systems dictates the physical properties, and symmetry is the determining factor for all electronic properties. This makes group theory a powerful tool in quantum mechanics to compute molecular properties. For inorganic compounds, the coordination geometry has been estimated as idealized polyhedra with high symmetry, which, through ligand field theory, provides predictive capabilities. However, real samples rarely have ideal symmetry, and although continuous shape measures (CShM) can be used to evaluate deviation from an ideal reference structure σideal, this often fails for lanthanide(III) complexes with high coordination numbers, no obvious choice of principal axes, and no obvious reference structure. In lanthanide complexes, the unique electronic structures and associated properties are intricately tied to the symmetry around the lanthanide center. Therefore, robust methodologies to evaluate and estimate point group symmetry are instrumental for building structure-property relationships. Here, we have demonstrated an algorithmic approach that orients a molecular structure Q in the best possible way to the symmetry axis of any given point group G and computes a deviation from the ideal symmetry σsym(G,Q). This approach does not compute the deviation from an ideal reference system, but the intrinsic deviation in the structure induced by symmetry operations. If the structure contains the symmetry operation, there is no deviation and σsym(G,Q) = 0. The σsym deviation is generated from all of the symmetry operation ÔS in a point group G using the most correct orientation of the sample structure in each group G. The best orientation is found by an algorithm that minimizes the orientation of the structure with respect to G. To demonstrate the methodology, we have investigated the structure and symmetry of 8- and 9-coordinated lanthanide(III) aqua complexes and correlated the luminescence from 3 europium(III) crystals to their actual symmetry. To document the methodology, the approach has been tested on 26 molecules with different symmetries. It was concluded that the method is robust and fully autonomous.
We present a comprehensive and updated Python-based open software to calculate continuous symmetry measures (CSMs) and their related continuous chirality measure (CCM) of molecules across chemistry. These descriptors are used to quantify distortion levels of molecular structures on a continuous scale and were proven insightful in numerous studies. The input information includes the coordinates of the molecular geometry and a desired cyclic symmetry point group (i.e., Cs, Ci, Cn, or Sn). The results include the coordinates of the nearest symmetric structure that belong to the desired symmetry point group, the permutation that defines the symmetry operation, the direction of the symmetry element in space, and a number, between zero and 100, representing the level of symmetry or chirality. Rather than treating symmetry as a binary property by which a structure is either symmetric or asymmetric, the CSM approach quantifies the level of gray between black and white and allows one to follow the course of change. The software can be downloaded from https://github.com/continuous-symmetry-measure/csm or used online at https://csm.ouproj.org.il.
Symmetry of proteins, an important source of their elegant structure and unique functions, is not as perfect as it may seem. In the framework of continuous symmetry, in which symmetry is no longer a binary yes/no property, such imperfections can be quantified and used as a global descriptor of the three-dimensional structure. We present an improved algorithm for calculating the continuous symmetry measure for proteins that takes into account their complete set of atoms including all side chains. Our method takes advantage of the protein sequence and the division into peptides in order to improve the accuracy and efficiency of the calculation over previous methods. The Hungarian algorithm is applied to solve the assignment problem and find the permutation that defines the symmetry operation. Analysis of the symmetry of several sets of protein homomers, with various degrees of rotational symmetry is presented. The new methodology lays the foundations for accurate, efficient and reliable large scale symmetry analysis of protein structure and can be used as a collective variable that describes changes of the protein geometry along various processes, both at the backbone level and for the complete protein structure.
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