Questioning Fundamental Principles of Organic Chemistry.zip
Creators: name: Yu, Zhongheng
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 340503
subject: Organic chemical synthesis
classificationCode: 340505
subject: Physical organic chemistry
classificationCode: 340701
subject: Computational chemistry

description: In Chapter 1, nine molecules, (N-Ar,N-methyl)-w-aminopolyenals (Ar: phenyl, 2-naphthyl, 2-anthracenyl), are synthesized. Their crystal structures and UV absorption frequencies are determined. Using the rule of homologous linearity, our experiments, along with theoretical geometry optimizations, reveal that conjugation between the aromatic ring (Ar-) and the amino group causes molecular distortion. The classical assumption of conjugation stabilization appears to be challengeable. In NBA-like species (Ar-N=CH-Ar’), the unusually large twist angle is an experimental phenomenon that classical structural theory cannot explain. In Chapter 2, eight NBA-like species with five- or six-membered heterocyclic rings and four substituted N,2,2-triphenylketene imines are synthesized, and their crystal structures are determined. For both synthesized and literature-derived NBA-like species, relaxed PES scans with an increasing torsion angle θ reveal intriguing results. The conformation with the abnormal large twist angle, despite having the greatest steric hindrance between groups Ar- and -N=CHAr’, is the most stable. These findings suggest that classical principles, such as conjugation stabilization and steric hindrance destabilization, should be reconsidered. As a result, a new π-σ energy decomposition procedure is developed based on an absolutely localized fragment molecular orbital basis set in Chapters 3, 4, and 5. This method shows that in NBA-like species, π-π, non-bonded σ-σ, and π-σ molecular orbital interactions are all destabilizing. The first two interactions drive molecular distortion, while the last one prevents the molecule from twisting. The largest distortion results from the balance of these interactions, thus confirming the legitimacy of our challenge. In Chapters 6, 8, and 12, the destabilizing conjugation energy effects between pairs of double bonds are found to be additive in polyenes but not in aromatic molecules. This discovery enables the creation of a virtual reference molecule for each aromatic compound, allowing the development of a purely theoretical, parameter-free method for accurately calculating aromatic energy. This has been a long-standing goal in theoretical chemistry. Crucially, our calculations show that the conjugation energy (1.4 kcal/mol) of butadiene is destabilizing, which challenges the classical view based on selectively chosen experimental heats of hydrogenation for butene isomers. This point is fundamental; otherwise, our theoretical framework would be invalid. Our method's accuracy and rationality should be validated by three essential benchmarks: the conjugation energy of cyclobutadiene must be destabilizing, the aromatic energy of benzene must be stabilizing, and the calculated values match experimental ones closely. The destabilizing conjugation energy of cyclobutadiene is 53.6 kcal/mol (experimental: 56 kcal/mol), and the stabilizing aromatic energy of benzene is -36.3 kcal/mol (experimental: -36 kcal/mol). This demonstrates the accuracy, rationality, and superiority of our method. The book further distinguishes between π-molecular orbital and π-electron delocalizations and applies our method to a wide range of molecules. These include five- and six-membered aromatic rings, polycyclic benzenoid hydrocarbons, [N]annulenes, strained aromatics, and substituted butadiene. Notably, it reveals that benzene’s D6h stability results from minimized nuclear repulsion. The distortion of the central ring in strained aromatics stems from conjugation with smaller rings. We also address controversies regarding the aromaticity of furan-like species and [N]annulenes, concluding that furan-like molecules are intermediate between aromatic and non-aromatic, while larger [N]annulenes (N &gt;18) behave more like polyenes, losing their aromatic or anti-aromatic character. These insights redefine the structural theory of organic chemistry.