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

Abstract

The correlation of the rotation about the C α −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 β −C α 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 β −C α 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. ψ/θ Scatter plots of the individual structure points and their averaging in ψ/θ av curves result in wavelike patterns with three maxima and minima and inversion symmetry at ψ = 0°and ±180 for a 360°rotation of C β about the C α −C′ bond. The pyramidalization of the sp 2 -hybridized group C α C i C o C o′ , 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.

Twofold and Threefold Sinusoidal Patterns in Coupled Molecular Motions of 184,025 Structures of Phenylethane, Nitroethane, and Carboxylate Derivatives

“…Thus, as in our previous analysis of carboxylates, carboxamides, ketones, etc., the ψ / θ av curve of 14,169 structures of C β -C α H 2 -Ph in Figure A proves the gearlike coupling of rotation about the bond C α –C i and pyramidalization of the group C α C i C o C o′ in a synchronized molecular motion. Surprisingly, the undulation of the ψ / θ av curve shows threefold symmetry, whereas in the substructure C β -C α H 2 -Ph, the twofold symmetry dominates.…”

“…The coupled molecular motion of rotation about the bond C α –C i and pyramidalization of the group C α C i C o C o′ , discussed above for phenylethane C β -C α H 2 -Ph, was described for the first time in refs , for carboxylates, carboxamides, ketones, etc. Dealing with 14,169 phenyls C β -C α H 2 -Ph, we came across other molecular motions, which are intimately coupled with each other.…”

“…In substituted acetates of the substructure C β -C α HX-C′(O)­O, a coupled molecular motion of rotation about the bond C α –C′ and pyramidalization of the sp 2 hybridized atom C′ had been observed. , With three open positions for substituents at C β and one open position at C α and the singly bonded oxygen atom, respectively, the substructure C β -C α HX-C′(O)­O included 84,572 structures retrieved from the Cambridge Structural Database (CSD).…”

“…Occurrence in percent (right ordinate). Reprinted with permission from ref . Copyright 2021 American Chemical Society.…”

“…In our previous studies, , we had included ortho -substituted phenyls C β -C α HX-C i (C o -Y)­(C 4 H 4 ) to keep the group C α C i C o C o′ chiral on pyramidalization. In the present paper, we expand our studies to 14,169 phenyls C β -C α H 2 -Ph with three open coordination positions at C β and 150,568 phenyls C β -C α HX-Ph with an additional open coordination position X at C α .…”