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Heteroaromatic species are commonly found in complex gaseous mixtures, from tobacco smoke to petroleum and asphaltene combustion products. At high temperatures, C–H bond rupture produces various dehydro radical isomers. We have used the spin–flip formulation of equation-of-motion coupled cluster theory with single and double substitutions (EOM-SF-CCSD) to characterize the energies and wave functions of the lowest lying singlet and triplet states of the diradical (2,3), (2,4), (2,5), and (3,4) di-dehydro isomers of pyrrole, furan, and thiophene. In all cases, these diradicals are minima on the broken-symmetry ωB97X-D/cc-pVDZ potential energy surface. In most cases, the diradical geometries distort to enhance through-space or through-bond coupling in the singlet states and to avoid Coulombic or exchange repulsion in the triplet states. EOM-SF-CCSD results indicate that all diradical isomers are two-configurational, closed shell singlet states. The only exceptions to this are for (2,3) and (2,4) thiophene and (2,3) pyrrole, which each contain more than two configurations. In all cases, the leading term in the multiconfigurational diradical wave function doubly occupies the symmetric radical σ orbital, indicative of either through-space or 1,3 through-bond coupling. We utilized the nucleus-independent chemical shift (NICS) approach to qualitatively assess aromaticity and find that this property varies and may be related to the energetic splittings in these diradical isomers. [ABSTRACT FROM AUTHOR]

We have analyzed the chemical bonding and reactivity in the cubic molecule octahydridosilsesquioxane, Si8H8O12, and its counterpart Ge8H8O12 by means of ab initio quantum chemical methods and group theory. Density functional theory and MP2 methods combined with the basis sets 6-311+G(d) and 6-311++G(2d,p) were used for geometry optimization and vibrational frequency analysis. The geometries of Si8H8O12 and Ge8H8O12 are unstable under Oh symmetry and distort to the rare Th molecular symmetry. The energy gained from this pseudo-Jahn–Teller distortion ranges from 0.78 to 6.14 kcal mol−1 depending on methodological treatment. The Fukui functions and the molecular electrostatic potential were both used as DFT-based reactivity descriptors. Our study shows that Si8H8O12 and Ge8H8O12 are both hard amphoteric molecules. The cavity within each cage is acidic and able to encapsulate hard small bases such as F−. The exterior of the cages is basic and can form stable exohedral complexes with hard acids, as in the case of H+. The insertion of F− in Si8H8O12 and Ge8H8O12 cages gives the most stable endohedral complexes of the series studied, characterized by formation energies of −3.50 and −3.45 eV at CAM-B3LYP/6-311+G(d) and −3.61 and −3.68 eV at the MP2/6-311++G(d,p) level, respectively. The calculated formation energies of the exohedral and endohedral complexes align with the DFT reactivity descriptor analysis. [ABSTRACT FROM AUTHOR]

The synthesis and characterization of three new isomeric dipyridoannulenes which have differing conjugation pathways between the substituent alkoxy donating groups and the pyridyl acceptor groups is reported. The molecules could be used as good metal binding candidates as the pyridine moiety could act as both an electron-acceptor and a site for metal coordination.

The synthesis, chemical properties and the characterization of trimeric maleimide clusters as homotrifunctional cross-linking reagents by classical mechanical conformational searching techniques are described. The results have provided useful information regarding the molecular shape of CD4 cellular receptors as well as the prehairpin intermediate involved in the HIV-cell fusion event.

A study explores the tuning of the Bergman cyclization by analyzing the rearrangement of two osmaenediynes and one rhodaenediyne by the introduction of metal fragments at its various positions. The activation energy of the rearrangement of the rhodaenediyne is found to be the same as that of the parent enediyne, hence making the study of the diradical nature of the resulting intermediates possible.

The conformational flexibility of a series of cage, basket, ladder, and tube polyhedral oligomeric silsesquixones (POSS) is examined using the Low Mode:Monte Carlo conformational search method in conjunction with the MM3*/GBSA(CHCl3) surface. Results indicate that, except for the ladder molecule, the incompletely condensed systems that are studied are relatively rigid.

The geometrics, structures and energetics of a series of unusual geodesic polyarenes are described. Symmetry considerations, bond length alternations and NICS value indicate that ground states of dicyclobuta[de,ij]naphthalene, dihydrodicyclobuta[de,ij]naphthalene and dihydrocyclopenta[cd,gh]pentalene are aromatic.

A set of molecular mechanics parameters for modeling carbohydrates in the context of the united atom AMBER* force field is developed using standard methods of empirical force field parameterization. The MC(JBW)/SD simulation method that facilitates interconversion between diastereomers by alternating between Monte Carlo and stochastic dynamics steps is used to calculate the anomeric ratios. The anomeric free energies generated are within the limits of the experimentally determined anomeric free energies in water.