Sitting above the maze: recent model discoveries in molecular science

Probing Intramolecular Interaction of Stereoisomers Using Computational Spectroscopy

Several model stereoisomers such as ferrocene (Fc), methoxyphenol, and furfural conformers are discussed. It was discovered that the Fc IR spectroscopic band(s) below 500cm−1 serve as fingerprints for eclipsed (splitting 17 (471–488)cm−1) and staggered Fc (splitting is ~2 (459–461)cm−1) in the gas phase. It is revealed that in the gas phase the dominance of the eclipsed Fc (D5h) at very low temperatures changes to a mixture of both eclipsed and staggered Fc when the temperature increases. However, in solvents such as CCl4, eclipsed Fc dominates at room temperature (300K) due to the additional solvation energy. Intramolecular interactions of organic model compounds such as methoxyphenols (guaiacol (GUA) and mequinol (MEQ)) and furfural, ionization energies such as the carbon 1s (core C1s), as well as valence binding energy spectra serve this purpose well. Hydrogen bonding alters the C1s binding energies of the methoxy carbon (C(7)) of anti-syn and anti-gauche conformers of GUA to 292.65 and 291.91eV, respectively. The trans and cis MEQ conformers, on the other hand, are nearly energy degenerate, whereas their dipole moments are significantly different: 2.66 Debye for cis and 0.63 Debye for trans-MEQ. Moreover, it is found that rotation around the Cring–OH and the Cring–OCH3 bonds differ in energy barrier height by ~0.50 kcal⋅mol−1. The Dyson orbital momentum profiles of the most different ionic states, 25a′ (0.35eV) and 3a′ (−0.33eV), between cis and trans-MEQ in outer valence space (which is measurable using electron momentum spectroscopy (EMS)), exhibit quantitative differences. Finally, the molecular switch from trans and cis-furfural engages with a small energy difference of 0.74 kcal mol−1, however, at the calculated C(3)(–H⋅⋅⋅O=C) site the C1s binding energy difference is 0.105eV (2.42 kcal mol−1) and the NMR chemical shift of the same carbon site is also significant; 7.58ppm from cis-furfural without hydrogen bonding.

Electronic structures of hexane isomers studied using quantum mechanics and graph theory

Electronic and topological properties of hexane ( C 6 H 14) and its five geometric isomers are systematically studied quantum mechanically using several techniques such as positron–electron annihilation gamma-ray spectra, C1s binding energy spectra and carbon nuclear magnetic resonance (NMR) spectra, as well as information derived from graph theory. It is revealed that the Doppler-shift in the gamma-ray spectra of the hexane isomers is in the vicinity of the n-hexane molecule with small structural dependency, in agreement with the fact that the measured Doppler-shifts of other linear alkanes are in the vicinity of hexane. The present study further reveals the electronic structures of hexane isomers, which are deeply rooted into the carbon core electrons, more than mere properties in the valence space. The calculations show that the highest occupied molecular orbitals (HOMOs) of the isomers exhibit less important roles in gamma-ray spectra; whereas the electron–positron annihilation is dominated by the electrons of the lowest occupied valence orbitals (LOVOs) and other valence electrons underneath the HOMO electrons, in agreement with previous findings. The present study further reveals that the C1s binding energies of the isomers exhibit association with the nodes of the isomers using graph theory. That is, more branched carbons likely engage with larger chemical shift, which is indicated by the largest eigenvalues (LEVs) of the adjacency matrix (AM) from graph theory. The chemical shift of the carbon NMR spectra is revealed by the LEVs of the Laplacian matrix (LM) obtained from chemical graph theory.

The d-electrons of Fe in ferrocene: the excess orbital energy spectrum (EOES)

The EOES (Δε_i=εE-Fci −εS-Fci) shows that the orbitals with significantly excess energies are Fe d-electron dominant.