Experimental and computational evidence for "double pancake bonds": the role of dispersion-corrected DFT methods in strongly dimerized 5-arl-1λ2, 3λ2-dithia-2,4,6-triazines.a λ

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Boeré, René T.
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ACS Publications
Crystal structures are reported for bicyclic 3CF3C6H4CN5S3 and monocyclic 3-CF3C6H4CN3S2, the latter of which is strongly dimerized in a cis-cofacial geometry [3-CF3C6H4CN3S2]2. The title compounds have previously been characterized in solution by NMR, displaying spectra that are consistent with the structure of [3CF3C6H4CN3S2]2 in the crystal with anti-oriented CF3 substituents. The interannular binding was investigated using density functional theory (DFT) methods. However, the DFT-optimized geometry spreads the aryl rings too far apart (centroid−centroid distances of ≥4.353 Å versus experimental distance of 3.850 Å). Significant improvements are obtained with dispersion-corrected DFT functionals B3LYPD3, B3LYP-D3BJ, M062X, and APFD using the 6-311+G(2d,p) basis set. However, all of these overbind the aryl rings with centroid−centroid distances of 3.612, 3.570, 3.526, and 3.511 Å, respectively. After selecting B3LYP-D3BJ/6-311+G(2d,p) as the best method, five alternative dimer geometries were tested, and all were found to be binding; however, anti cofacial-4 (matching the structure in the solid state) is the most stable. Computed energies of the remainder are as follows: +7.0 kJ mol−1 (syn-cofacial-5), +26.7 kJ mol−1 (anti-cofacial-64), +27.0 kJ mol−1 (syn-cofacial-150), +102.0 kJ mol−1 (S,S-antarafacial), and +103.7 kJ mol−1 (S,N-antarafacial), where the suffixes are torsional angles around the CN3S2 thiazyl ring centroids. The binding in the four most stable cofacial dimers may be described by “double pancake bonding”.
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Double pancake bonding
Boeré, R. T. (2018). Experimental and computational evidence for "double pancake bonds": The rold of dispersion-corrected DFT methods in strongly dimerized 5-arl-1[lambda]2, 3[lambda]2-dithia-2,4,6-triazines. ACS Omega, 3, 18170-18180. DOI:10.1021/acsomega.8b03211