Halogen bonding (R-X···Y) is a qualitative analogue of hydrogen bonding that may prove useful in the rational design of artificial proteins and nucleotides. We explore halogen-bonded DNA base pairs containing modified guanine, cytosine, adenine and thymine nucleosides. The structures and stabilities of the halogenated systems are compared to the normal hydrogen bonded base pairs. In most cases, energetically stable, coplanar structures are identified. In the most favorable cases, halogenated base pair stabilities are within 2 kcal mol(-1) of the hydrogen bonded analogues. Among the halogens X = Cl, Br, and I, bromine is best suited for inclusion in these biological systems because it possesses the best combination of polarizability and steric suitability. We find that the most stable structures result from a single substitution of a hydrogen bond for a halogen bond in dA:dT and dG:dC base pairs, which allows 1 or 2 hydrogen bonds, respectively, to complement the halogen bond.

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The electronic interaction between confined pairs of He atoms in the C(20)H(20) dodecahedrane cage is analyzed. The He-He distance is only 1.265 A, a separation that is less than half the He-He distance in the free He dimer. The energy difference between the possible isomers is negligible (less than 0.15 kcal mol(-1)), illustrating that there is a nearly free precession movement of the He(2) fragment around its midpoint in the cage. We consider that a study of inclusion complexes, such as the case we have selected and other systems that involve artificially compressed molecular fragments, are useful reference points in testing and extending our understanding of the bonding capabilities of otherwise unreactive or unstable species. A key observation about bonding that emerges uniquely from endohedral (confinement) complexes is that a short internuclear separation does not necessarily imply the existence of a chemical bond.

Connections between the structures of Group 12 dihalides in their vapor and crystal phases are sought and discussed. The molecular structures of all monomers and dimers (MX(2): M=Zn, Cd, Hg and X=F, Cl, Br, I) were calculated at the density functional B3PW91 and MP2 computational levels. All the monomers are linear, with the mercury dihalide molecules having shorter bonds than their cadmium analogues; the ZnX(2) and CdX(2) structures are similar. The shorter Hg-X distances are traced back to relativistic effects. For the dimers, many possible geometrical arrangements were considered. The zinc and cadmium dihalide dimers have the usual D(2h)-symmetry geometry, whereas the mercury dihalide dimers are loosely-bound units with C(2h) symmetry. The origins of this C(2h) structure are discussed from different points of view, including frontier orbital interactions. The crystals of Group 12 dihalides span a wide range of structure types, from three-dimensional extended solids to molecular crystals. There is an obvious connection between the structures and characteristics of monomers, their dimers, and the crystals they form. The similarities as well as startling differences from the Group 2 dihalides are analyzed.

Bonding interactions between an electron-deficient region (a sigma-hole) on M and electron donors in MF4-Base complexes, where M = C, Si, Ge, Sn, and Pb, are examined and rationalized. These interactions are seen to transition from weak primarily noncovalent interactions for all bases when M = C to stronger primarily covalent bonds in adducts as the valence shell expands for the heavier M atoms. For M = Ge, Sn, and Pb, the complexes are particularly stable. The consistent axial preference in these systems is anticipated by previous studies and is readily explained from the vantage point of sigma-hole interactions. A series of bound complexes of common bases such as pyridine, tetrahydrofuran, and water are identified, some of which are even more stable than the SiF4·NH3 and SiF4·N(CH3)3 complexes that have already been identified experimentally. Sigma-hole bonding to di- and poly-substituted central atoms, perhaps on par with halogen bonding, is expected to become increasingly important as an ordering interaction in materials science and engineering. Group 14 compounds have distinct advantages in this respect.

The polarizable valence-state-atoms-in-molecules (pVSAM) model describes the electron-pair bond in A-B molecules by superposing core-polarized A + B -, A -B + , and A:B structures, whose weights are determined by electronegativity equalization. The polarizable valence state potential energy curve (pVS-PEC) is derived through the systematic improvement of the valence state potential energy curve (VS-PEC) [Gardner, D. O. N.; von Szentpa ´ly, L. J. Phys. Chem. A 1999, 103, 9313] and is given as (-λR). The first bracketed term contains the Coulomb, charge-induced dipole, and induced dipole-induced dipole terms, derived from weighted ionic and covalent bond-charge contributions. The potential is tested on a broad variety of homonuclear diatoms and heteronuclear halides and hydrides (a total of 52 molecules). The accuracies of the dimensionless vibration-rotation coupling constant (F) and the anharmonicity constant (G) for the halides of the alkali and coinage metals are significantly better than those of the Morse, Rydberg, simple bond-charge, and Rittner potentials. Adding core polarization to the VS-PEC reduces the average unsigned errors in the spectroscopic constants of 47 diatomic molecules from 17.1% to 7.5% in F and 18.9% to 7.8% in G, whereas those of the Morse potential amount to 32.6% and 31.4%, respectively.

The existence and persistence of five-fold (quintuple) bonding in isomers of model RMMR molecules of quite different geometry are examined theoretically. The molecules studied are RMMR, with R = H, F, Cl, Br, CN, and CH3; M = Cr, Mo, and W. The potential energy surface of these molecules is quite complex, containing two, three, even four local minima. The structural preferences in these molecules are rationalized, and electronic factors responsible for these preferences are elucidated. The linear geometry is always a minimum, but almost never the global minimum; there is a definite preference in RMMR for either a trans-bent conformation or perturbations of the trans-bent isomer with at least one of the R groups in a bridging position about the MM bond. The potential energy surface of these RMMR molecules is relatively flat, the lowest energy conformation being that which for a given molecule attains the best compromise between maximization of the MM bonding and minimization of orbital interactions that are MR antibonding. A surprising low-symmetry C(s) structure is identified, which along with the trans-bent isomer is one of the two most popular choices for the global minimum. Regardless of what isomer of the RMMR molecule is preferred, the MM quintuple bond persists.

The link between structural preferences in the monomers, dimers, and extended solid-state structures of the group 2 dihalides (MX(2): M = Be, Mg, Ca, Sr, Ba and X = F, Cl, Br, I) is examined theoretically. The question posed is how well are geometric properties of the gas-phase MX(2) monomers and lower order oligomers "remembered" in the corresponding MX(2) solids. Significant links between the bending in the MX(2) monomers and the D(2)(h)()/C(3)(v)() M(2)X(4) dimer structures are identified. At the B3LYP computational level, the monomers that are bent prefer the C(3)(v)() triply bridged geometry, while the rigid linear molecules prefer a D(2)(h)() doubly bridged structure. Quasilinear or floppy monomers show, in general, only a weak preference for either the D(2)(h)() or the C(3)(v)() dimer structure. A frontier orbital perspective, looking at the interaction of monomer units as led by a donor-acceptor interaction, proves to be a useful way to think about the monomer-oligomer relationships. There is also a relationship between the structural trends in these two (MX(2) and M(2)X(4)) series of molecular structures and the prevalent structure types in the group 2 dihalide solids. The most bent monomers condense to form the high coordination number fluorite and PbCl(2) structure types. The rigidly linear monomers condense to form extended solids with low coordination numbers, 4 or 6. The reasons for these correlations are explored.