Rotation about a Covalent Bond and Pyramidalization of an Adjacent sp2 Center are a Synchronized Molecular Motion

The correlation of the rotation about the C-alpha-C' bond and the pyramidalization of the sp(2)-hybridized carbon atom C' and its three bonding partners to a flattened tetrahedron in the substructure C-beta-C alpha H-C'(=O)-OMe of substituted methyl acetates revealed that the two processes are not independent of each other but parts of a common molecular motion, as outlined in the preceding back-to-back paper. In the present study, we generalized the substructure to X-beta-C alpha H-C'(=Y)-Z with X, Y, and Z = O, N, C, and S, extending the analysis to several hundred thousand structures of the type carboxylates, carboxamides, ketones, imines, olefins, peptides, lactates, carbothioates, and phenyl derivatives, retrieved from the Cambridge Structural Database. psi/theta Scatter plots of the individual structure points and their averaging in psi/theta(av) curves result in wavelike patterns with three maxima and minima and inversion symmetry at psi = 0 degrees and +/- 180 for a 360 degrees rotation of C-beta about the C-alpha-C' bond. The pyramidalization of the sp(2)-hybridized group C alpha CiCoCo', which is part of the aromatic system, even disturbs the planarity of phenyl rings. Density functional theory calculations confirm the results of the CSD search.

Automated summary

The study revealed that the rotation about the C-alpha-C' bond and the pyramidalization of the sp(2)-hybridized carbon atom are part of a common molecular motion, extending the analysis to various types of compounds. Scatter plots of psi/theta for individual structures showed wavelike patterns during a 360-degree rotation of Cβ about the C-alpha-C' bond, and the pyramidalization of the sp(2)-hybridized group can disrupt the planarity of phenyl rings. Density functional theory calculations confirmed the findings from the CSD search.