Kelling J. Donald

Influence of Endohedral Confinement on the Electronic Interaction between He atoms: A He2@C20H20 Case Study

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.

Halogen Bonding in DNA Base Pairs

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.

Group 12 dihalides: structural predilections from gases to solids.

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.

CBe5E− (E = Al, Ga, In, Tl): planar pentacoordinate carbon in heptaatomic clusters

A series of clusters with the general formula CBe(5)E(-) (E = Al, Ga, In, Tl) are theoretically shown to have a planar pentacoordinate carbon atom. The structures show a simple and rigid topological framework-a planar EBe(4) ring surrounding a C center, with one of the ring Be-Be bonds capped in-plane by a fifth Be atom. The system is stabilized by a network of multicenter σ bonds in which the central C atom is the acceptor, and π systems as well by which the C atom donates charge to the Be and E atoms that encircle it.

Tuning σ-Holes: Charge Redistribution in the Heavy (Group 14) Analogues of Simple and Mixed Halomethanes Can Impose Strong Propensities for Halogen Bonding

Halogen bonding between halide sites (in substituted organic molecules or inorganic halides) and Lewis bases is a rapidly progressing area of exploration. Investigations of this phenomenon have improved our understanding of weak intermolecular interactions and suggested new possibilities in supramolecular chemistry and crystal engineering. The capacity for halogen bonding is investigated at the MP2(full) level of theory for 100 compounds, including all 80 MH(4-n)X(n) systems (M = C, Si, Ge, Sn, and Pb; X = F, Cl, Br, and I). The charge redistribution in these molecules and the (in)stability of the sigma-hole at X as a function of M and n are catalogued and examined. For the mixed MH(3-m)F(m)I compounds, we identify a complicated dependence of the relative halogen bond strengths on M and m. For m = 0, for example, the H(3)C-I----NH(3) halogen bond is 6.6 times stronger than the H(3)Pb-I----NH(3) bond. When m = 3, however, the F(3)Pb-I----NH(3) bond is shorter and approximately 1.6 times stronger than the F(3)C-I----NH(3) bond. This substituent-induced reversal in the relative strengths of halogen bond energies is explained.

Stabilizing carbon-lithium stars

We have explored in silico the potential energy surfaces of the C(5)Li(n)(n-6) (n = 5, 6, and 7) clusters using the Gradient Embedded Genetic Algorithm (GEGA) and other computational strategies. The most stable forms of C(5)Li(5)(-) and C(5)Li(6) are two carbon chains linked by two lithium atoms in a persistent seven membered ring capped by two Li atoms. The other Li atoms are arrayed on the edge of the seven membered ring. In contrast, the global minimum structure for C(5)Li(7)(+) is a bicapped star of D(5h) symmetry. The molecular orbital analysis and computed magnetic field data suggest that electron delocalization, as well as the saturation of the apical positions of the five-membered carbon ring with lithium atoms in C(5)Li(7)(+) plays a key role in the stabilization of the carbon-lithium star. In fact, the planar star sub-structure for the carbon ring are unstable without the apical caps. This is also what has been found for the Si analogues. The split of the B(ind)(z) in its σ- and π-contribution indicates that C(5)Li(7)(+) is a π-aromatic and σ-nonaromatic system.

The Weak Helps the Strong: Sigma-Holes and the Stability of MF4·Base Complexes

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.

Isomerization energy decomposition analysis for highly ionic systems: Case study of starlike E5Li7+ clusters

The most stable forms of E(5)Li(7)(+) (E = Ge, Sn, and Pb) have been explored by means of a stochastic search of their potential-energy surfaces by using the gradient embedded genetic algorithm (GEGA). The preferred isomer of the Ge(5)Li(7)(+) ion is a slightly distorted analogue of the D(5h) three-dimensional seven-pointed starlike structure adopted by the lighter C(5)Li(7)(+) and Si(5)Li(7)(+) clusters. In contrast, the preferred structures for Sn(5)Li(7)(+) and Pb(5)Li(7)(+) are quite different. By starting from the starlike arrangement, corresponding lowest-energy structures are generated by migration of one of the E atoms out of the plane with the a corresponding rearrangement of the Li atoms. To understand these structural preferences, we propose a new energy decomposition analysis based on isomerizations (isomerization energy decomposition analysis (IEDA)), which enable us to extract energetic information from isomerization between structures, mainly from highly charged fragments.

Halogen Bonding: Unifying Perspectives on Organic and Inorganic Cases

We find for distinct classes of halogen bonded complexes (MF3-X···Y) that the ab initio BSSE-corrected binding energies (ΔE) and enthalpies (ΔH) are predicted by functions of the form y = A/r(n) + C. Here X is a halogen atom, Y is a base, r is the X···Y separation, and A, n, and C are constants. The actual value of n (5.5 < n < 7.0 for ΔE) for each class is determined evidently by the availability of the lone pairs on the base and is insensitive to M such that all of the complexes of a given base fall on the same curve for y versus r. Remarkably, several bases show the same behavior in some cases such that just three curves account for 55 MF3I···Y complexes of 11 bases, where M = C, Si, Ge, Sn, and Pb. Two additional bases, THF and NF3, which form especially strong and weak complexes, respectively, are in classes by themselves. Anomalous modes of halogen bonding are identified; in particular, furan forms sigma-hole complexes via carbons 2 and 3 (through the π system) in the ring in preference to the oxygen site. These results are in line with experimental observations for furan-dihalogen complexes, and several other small MF3I···Y pairs are proposed in this work for experimental interrogation. Instead of halogen bonding, CF4 tends to form weak sigma-hole bonds to bases via the polarized central carbon atom, and new examples of such pro-dative interactions to carbon in CF4 are identified in this work. We find that GeF3I and SnF3I form I···Y halogen bonds of comparable energies to those formed by the smaller and better studied CF3I. PbF3I forms the strongest halogen bond regardless of the identity of the base; SiF3I consistently forms the weakest link.

Dynamical behavior of boron clusters

Several of the lowest energy structures of small and medium sized boron clusters are two-dimensional systems made up of a pair of concentric rings. In some cases, the barriers to the rotation of one of those rings relative to the other are remarkably low. We find that a combination of electronic and geometrical factors, including apparently the relative sizes and symmetries of the inner and outer rings, are decisive for the diminished barriers to in-plane rotation in these two dimensional clusters. A sufficiently large outer ring is important; for instance, expansion of the outer ring by a single atom may reduce the barrier significantly. A crucial factor for an apparent rotation is that the σ-skeleton of the individual rings remains essentially intact during the rotation. Finally, the transition state for the rotation of the inner ring comprises the transformation of a square into a diamond, which may be linked to a mechanism suggested decades ago for the isomerization of carboranes and boranes.