Symmetry-Binding Correlations of Crown Ether Complexes with Li+ and Na. ACS Omega 2021;6:19233-19237. [PMID: 34337261 PMCID: PMC8320112 DOI: 10.1021/acsomega.1c02684]

CSM Software: Continuous Symmetry and Chirality Measures for Quantitative Structural Analysis

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.

Continuous symmetry and chirality measures: approximate algorithms for large molecular structures

Quantifying imperfect symmetry of molecules can help explore the sources, roles and extent of structural distortion. Based on the established methodology of continuous symmetry and chirality measures, we develop a set of three-dimensional molecular descriptors to estimate distortion of large structures. These three-dimensional geometrical descriptors quantify the gap between the desirable symmetry (or chirality) and the actual one. They are global parameters of the molecular geometry, intuitively defined, and have the ability to detect even minute structural changes of a given molecule across chemistry, including organic, inorganic, and biochemical systems. Application of these methods to large structures is challenging due to countless permutations that are involved in the symmetry operations and have to be accounted for. Our approach focuses on iteratively finding the approximate direction of the symmetry element in the three-dimensional space, and the relevant permutation. Major algorithmic improvements over previous versions are described, showing increased accuracy, reliability and structure preservation. The new algorithms are tested for three sets of molecular structures including pillar[5]arene complexes with Li+, C100 fullerenes, and large unit cells of metal organic frameworks. These developments complement our recent algorithms for calculating continuous symmetry and chirality measures for small molecules as well as protein homomers, and simplify the usage of the full set of measures for various research goals, in molecular modeling, QSAR and cheminformatics.

Cationic Effects on the Structural Dynamics of the Metal Ion-Crown Ether Complexes Investigated by Ultrafast Infrared Spectroscopy

It is usually believed that the binding affinity and selectivity of an alkali metal ion with crown ether are defined by the size matching model. However, the underlying mechanism of the specific host-guest interactions and the structural dynamics of the metal ions confined in the cavity of the crown ethers in the solutions are still not clear. In this report, a series of alkali thiocyanate salts (XSCN; X = Li, Na, K, and Cs) complexed with 18-crown-6 (a typical crown ether) in the chloroform solutions were studied by the polarization-selective infrared pump-probe spectroscopy and the ultrafast two-dimensional infrared (2D IR) spectroscopy. The SCN^- counteranions were employed as the local vibrational probe to reveal the specific host-guest interactions in the crown ether complexes. The rotational dynamics and spectral diffusion of SCN^- vibration were both measured by ultrafast IR spectroscopy, and it was found that the metal cations hosted by the crown ethers can have a pronounced effect on the rotational dynamics of the counteranions. The reorientational time constants of the SCN^- vibration in the complexation follow the order Li⁺ > Na⁺ > K⁺ ≃ Cs⁺. More importantly, the spectral diffusion dynamics of SCN^-, which quantifies the decay of the correlation of the frequency fluctuations in the complexation, was also affected by the metal ions but showed a different order of cationic effect. A detailed analysis of the 2D IR data showed that the spectral diffusion of SCN^- counteranion clearly decayed with two different time scales in the complex of 18-crown-6 with K⁺. The 3-4-fold slowdown in spectral diffusion indicated that the fluctuation of SCN^- vibrational transition frequency was strongly affected by the K⁺ cation due to the geometric constraint imposed by the crown ether. The results should help the researchers to unravel the specific host-guest interactions and further reveal the origination of the binding selectivity of crown ether for metal cations in the condensed phases from the perspective of structural dynamics.