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Structures of conformers of bis(toluene)chromium(0) (1a, 1b, 1c и 1d) were studied using MP2 and B97-1 methods together with all-electron 6-311++G(d,p), cc-pVTZ, and QZVPP basis sets for C and H atoms and def2- QZVPP for Cr atom. Methyl groups in trans-conformer 1c and cis-conformer 1d are inverted with respect to those in trans-conformer 1a and cis-conformer 1b, respectively. The quantum theory of atoms in molecules (QTAIM) and NBO theory are used for analysis of bonding of toluene molecules with Cr(0) atom and different second order intramolecular interactions in 1a – 1d. Attractive and repulsive interactions between hydrogen atoms of methyl groups of two toluene molecules in 1b and 1d are analyzed. For all conformers interaction of the ring hydrogen atoms as well as hydrogen atoms of methyl groups with Cr atom, Cr-C and other bonds is discussed. The QTAIM structures of the conformers were found to depend on basis set size. This dependency can result in arbitrary choice of any QTAIM structure. Other drawbacks of the QTAIM in the analysis of closed shell interactions in 1a – 1d are also discussed.