The geometries, proton affinities, and relative energies of protonated digermane (Ge₂H₇⁺), distannane (Sn₂H₇⁺), and diplumbane (Pb₂H₇⁺) have been investigated by density functional theory using the correlation-consistent cc-pVnZ-PP basis sets (n = D, T, Q). The results of the caluclations are consistent with the very limited experimental and theoretical results that are available. The lowest-lying structure of Ge₂H₇⁺ is predicted to have C₂ symmetry with a bent 3-center-2-electron Ge–H–Ge bridge, analogous to Si₂H₇⁺. For Sn₂H₇⁺ and Pb₂H₇⁺, the lowest-lying structures are predicted to be different, with a D_3d structure for Sn₂H₇⁺ and a C₁ structure for Pb₂H₇⁺. The predicted proton affinities decrease in the order Pb₂H₆ (9.84 eV) > Sn₂H₆ (8.48 eV) > Ge₂H₆ (8.11 eV) > Si₂H₆ (7.72 eV) > C₂H₆ (6.18 eV).

Carbon-donated hydrogen bonds (CDHBs) are weak forms of hydrogen bonding (0.5–1.0 kcal mol⁻¹) that are difficult to detect, and thus their roles in the structure and functionality of chemical systems often go unrecognized. Utilizing a computational approach, the existence of a structurally significant CDHB in the medically relevant protein Streptococcus pneumoniae hyaluronate lyase (SpnHL) is affirmed. The structure of a tetrapeptide fragment model containing the CDHB was optimized with second-order perturbation theory. From this, a CDHB with bond distance and angle consistent with previously discovered CDHBs and comparable to neighboring traditional HBs in the fragment model was found. The CDHB competes with another donor T253 OH, whereby the two alternate in strength between protein conformations, imbuing αHelix 3 appreciable flexibility. The CDHB seems to exist in spite of torsional and steric strain on the donor methyl group. It is postulated that the CDHB could aid in either counteracting the macrodipole of αHelix 3 or protecting the A249 CO from destabilizing interactions with the adjacent solvent. Employing the energy gradients from the optimization, the torque generated by the fragment model was computed, which accurately predicts the direction of rotation of αHelix 3 observed from experiment. A strongly correlated motion between αHelix 3 and αHelices 2, 4, and 5 was noted, which the interactions of the fragment model help drive by generating a torque much larger than necessary to rotate just αHelix 3. Considering these results, we conclude that CDHBs should be considered as possible beneficial components of chemical and biological phenomena.

Germanium has been a central feature in the renaissance of main-group inorganic chemistry. Herein, we present the stationary-point geometries of tetragermacyclobutadiene and its related isomers on the singlet potential energy surface at the CCSD(T)/cc-pVTZ level of theory. Three of these 12 structures are reported for the first time and one of them is predicted to lie only 0.4 kcal mol⁻¹ above the previously reported global minimum. Focal-point analyses has provided electronic energies at the CCSD(T) level of theory, which are extrapolated to the complete basis-set limit and demonstrate the convergence behavior of the electronic energies with improving levels of theory and increasing basis-set size. The lowest-energy structure is the bicyclic structure, which lies 35 kcal mol⁻¹ below the “all-Ge” cyclobutadiene structure. The reaction energies for the association of known Ge hydrides (e.g., digermene) to form Ge₄H₄ indicate that Ge₄H₄ could be observed experimentally. We investigate the bonding patterns by examining the frontier molecular orbitals. Our results demonstrate that: 1) the cyclic isomers of (GeH)₄ distort to maximize the mixing of the p orbitals that are involved in the π system of tetragermacyclobutadiene and 2) the lowest-energy isomers exhibit unusual bonding arrangements (e.g., bridging H bonds) that maximize the nonbonding electron density at the Ge centers.

Several possible mechanisms underlying isoguanine formation when OH radical attacks the C₂ position of adenine (A) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A⋅⋅⋅OH reactant complexes is formed, leading to C₂H₂ bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG 1 or isoG 2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol–keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20 kcal mol⁻¹, indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH^.isoG+H^. reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG 1 has the lowest energy. Our findings explain why only the N₁H and O₂H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.

Recent high-resolution spectroscopic studies by Merritt, Bondybey, and Heaven (Science2009, 324, 1548) have heightened the anticipation that small beryllium clusters will soon be observed in the laboratory. Beryllium clusters are important discrete models for the theoretical study of metals. The trigonal bipyramidal Be₅ molecule is studied using high-level coupled cluster methods. We obtain the optimized geometry, atomization and dissociation energies, and vibrational frequencies. The c∼CCSDT(Q) method is employed to compute the atomization and dissociation energies. In this approach, complete basis set (CBS) extrapolations at the CCSD(T) level of theory are combined with an additive correction for the effect of iterative triple and perturbative quadruple excitations. Harmonic vibrational frequencies are obtained using analytic gradients computed at the CCSD(T) level of theory. We report an atomization energy of 129.6 kcal mol⁻¹ at the trigonal bipyramid global minimum geometry. The Be₅Be₄+Be dissociation energy is predicted to be 39.5 kcal mol⁻¹. The analogous dissociation energies for the smaller beryllium clusters are 64.0 kcal mol⁻¹ (Be₄Be₃+Be), 24.2 kcal mol⁻¹ (Be₃Be₂+Be), and 2.7 kcal mol⁻¹ (Be₂Be+Be). The trigonal bipyramidal Be₅ structure has an equatorial–equatorial bond length of 2.000 Å and an axial–equatorial distance of 2.060 Å. Harmonic frequencies of 730, 611, 456, 583, 488, and 338 cm⁻¹ are obtained at the CCSD(T)/cc-pCVQZ level of theory. Quadruple excitations are found to make noticeable contributions to the energetics of the pentamer, which exhibits a significant level of static correlation.