MRMP2, CCSD(T), and DFT Calculations of the Isomerization Barriers for the Disrotatory and Conrotatory Isomerizations of 3-Aza-3-ium-dihydrobenzvalene, 3,4-Diaza-3-ium-dihydrobenzvalene, and 3,4-Diaza-diium-dihydrobenzvalene.

The isomerizations of 3-aza-3-ium-dihydrobenzvalene, 3,4-diaza-3-ium-dihydrobenzvalene, and 3,4-diaza-diium-dihydrobenzvalene to their respective cyclic-diene products were studied using electronic structure methods with a multiconfigurational wave function and several single reference methods. Transition states for both the allowed (conrotatory) and forbidden (disrotatory) pathways were located. The conrotatory pathways of each structure all proceed through a cyclic intermediate with a trans double bond in the ring: this trans double bond destroys the aromatic stabilization of the π electrons due to poor orbital overlap between the cis and trans π bonds. The 3,4-diaza-3-ium-dihydrobenzvalene structure has C1 symmetry, and there are four separate allowed and forbidden pathways for this structure. The 3-aza-3-ium-dihydrobenzvalene structure is Cs symmetric, and there are two separate allowed and forbidden pathways for this structure. For 3,4-diaza-3,4-diium-dihydrobenzvalene, there was a single allowed and single forbidden pathway due to the C2v symmetry. The separation of the barrier heights for all three molecules was studied, and we found the difference in activation barriers for the lowest allowed and lowest forbidden pathways in 3,4-diaza-3-ium-dihydrobenzvalene, 3-aza-3-ium-dihydrobenzvalene, and 3,4-diaza-diium-dihydrobenzvalene to be 9.1, 7.4, and 3.7 kcal/mol, respectively. The allowed and forbidden barriers of 3,4-diaza-diium-dihydrobenzvalene were separated by 3.7 kcal/mol, which is considerably less than the 12-15 kcal/mol expected based on the orbital symmetry rules. The addition of the secondary ammonium group tends to shift the conrotatory and disrotatory barriers up in energy (∼12-14 kcal/mol (conrotatory) and 5-10 kcal/mol (disrotatory) per secondary NH2 group) relative to the barriers of dihydrobenzvalene, but there is negligible effect on E,Z to Z,Z isomerization barriers, which remain in the expected range of greater than 4 kcal/mol.

Examination of tyrosine/adenine stacking interactions in protein complexes.

The π-stacking interactions between tyrosine amino acid side chains and adenine-bearing ligands are examined. Crystalline protein structures from the protein data bank (PDB) exhibiting face-to-face tyrosine/adenine arrangements were used to construct 20 unique 4-methylphenol/N9-methyladenine (p-cresol/9MeA) model systems. Full geometry optimization of the 20 crystal structures with the M06-2X density functional theory method identified 11 unique low-energy conformations. CCSD(T) complete basis set (CBS) limit interaction energies were estimated for all of the structures to determine the magnitude of the interaction between the two ring systems. CCSD(T) computations with double-ζ basis sets (e.g., 6-31G*(0.25) and aug-cc-pVDZ) indicate that the MP2 method overbinds by as much as 3.07 kcal mol(-1) for the crystal structures and 3.90 kcal mol(-1) for the optimized structures. In the 20 crystal structures, the estimated CCSD(T) CBS limit interaction energy ranges from -4.00 to -6.83 kcal mol(-1), with an average interaction energy of -5.47 kcal mol(-1), values remarkably similar to the corresponding data for phenylalanine/adenine stacking interactions. Geometry optimization significantly increases the interaction energies of the p-cresol/9MeA model systems. The average estimated CCSD(T) CBS limit interaction energy of the 11 optimized structures is 3.23 kcal mol(-1) larger than that for the 20 crystal structures.

Hydrocarbon/Water Interactions: Encouraging Energetics and Structures from DFT but Disconcerting Discrepancies for Hessian Indices.

In this work, ab initio electronic structure computations have been used to systematically examine the structures and energetics of nine small hydrocarbon molecules interacting with water. Full geometry optimizations and harmonic vibrational frequency calculations were performed on 30 unique dimer configurations with the MP2 method and a triple-ζ correlation consistent basis set (cc-pVTZ for H and aug-cc-pVTZ for C and O, denoted haTZ). Three different estimates of the CCSD(T) complete basis set (CBS) limit interaction energies were determined for all 30 MP2 optimized hydrocarbon/water structures, and they never deviate from their mean by more than 0.07 kcal mol(-1). MP2 and CCSD(T) interaction energies are virtually identical (within 0.05 kcal mol(-1)) for dimer configurations primarily exhibiting CH···O and OH···C type interactions, but MP2 overbinds appreciably in some dimers that exhibited OH···π type interactions, by as much as 0.3 to 0.4 kcal mol(-1) (or ≈10%) for the unsaturated cyclic hydrocarbons examined (1,3-cyclobutadiene, 1,3-cyclopentadiene, and benzene). Four density functional theory (DFT) methods (B3LYP, B97-D, ωB97X-D, and M06-2X) were also applied to all 30 systems with the haTZ basis set to compare optimized structures, energetics, and numbers of imaginary vibrational frequencies (ni). The B97-D, ωB97X-D, and M06-2X functionals provide quite reasonable structures and energetics, which is consistent with other studies. This work, however, finds that all 4 DFT methods examined struggle to reliably characterize these potential energy surfaces (PESs). For example, the values of ni from the DFT frequency calculations differed from the corresponding MP2 results for approximately one-third of the stationary points located.

Effects of Heterogeneity in Small π-Type Dimers: Homogeneous and Mixed Dimers of Diacetylene and Cyanogen.

The homo- and heterogeneous dimers of diacetylene (H-C≡C-C≡C-H) and cyanogen (N≡C-C≡N) were studied using ab initio electronic structure computations to probe the effects of heterogeneity on noncovalent interactions between systems with delocalized π electron networks. Full geometry optimizations and harmonic vibrational frequencies were performed using the robust coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) method with the triple-ζ plus 2 sets of polarization functions TZ2P(f,d)++ basis set. Seven basic configurations were examined for each dimer (cross, stacked, parallel-slipped, parallel-tipped, linear, T-shaped and Y-shaped), but only four stationary points were identified on the potential energy surfaces (PESs) of the homogeneous cyanogen dimer and the mixed diacetylene/cyanogen dimer. Six previously characterized stationary points on the diacetylene dimer PES were re-examined with the CCSD(T) method and the TZ2P(f,d)++ basis set for consistency. Second-order Møller-Plesset perturbation theory (MP2) and CCSD(T) complete basis set (CBS) limit interaction energies were estimated using the explicitly correlated MP2-F12 and CCSD(T)-F12 methods in conjunction with the VQZ-F12 basis set. On the cyanogen dimer PES, the C2v T-shaped structure is the only minimum, with an average electronic interaction energy, Eint, of -1.96 kcal mol(-1) at the CCSD(T) CBS limit. The Cs Y-shaped structure (in agreement with previous results) is the global minimum on the diacetylene dimer PES, having a mean CCSD(T) CBS limit Eint of -1.75 kcal mol(-1). Three low-lying minima have been identified on the diacetylene/cyanogen dimer PES, a C∞v linear, a C2v cross, and a Cs parallel-slipped structure with average CCSD(T) CBS limit interaction energies of -2.00, -2.16, and -2.45 kcal mol(-1), respectively.

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations.

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.