Non-Born-Oppenheimer treatment of the H2 Hookean molecule

We show that the exact non-Born-Oppenheimer Schrodinger equation for the Hookean diatomic molecule H2 (a two-proton, two-electron system where the electron-proton interaction is harmonic while the proton-proton and electron-electron interactions are Coulombic) can be decoupled into equations describing the relative motion of the electrons, the relative motion of nuclei, the motion of a collective mode representing a three-dimensional harmonic oscillator, and the motion of a free particle expressed as a linear combination of the individual center-of-mass coordinates of the nuclei and electrons. Analytic solutions to the relative motion of electrons can be readily obtained for the given values of the harmonic coupling constant. However, exact analytic solutions to the equation for the relative motion of the nuclei cannot be obtained simultaneously due to the fact that the harmonic constants in these two equations are coupled. For this reason, we present for the relative nuclear motion approximate analytic wave functions, one of them obtained variationally and the other by a series solution where the coefficients are determined recursively. We also explore a variational solution to the Taylor-series expansion of the nuclear interaction potential. Properties of the electronic and nuclear intracule densities are examined at different values of the coupling constant. An interesting result of the present non-Born-Oppenheimer treatment of this harmonic model is the fact that the relative nuclear motion occurs in a highly correlated regime. This leads in a natural way to a spatial localization of the nuclei akin to Wigner electronic crystallization.     

Water-promoted hydrolysis of a highly twisted amide: rate acceleration caused by the twist of the amide bond

The water-promoted hydrolysis of a highly twisted amide is studied using density functional theory in conjunction with a continuum dielectric method to introduce bulk solvent effects. The aim of these studies is to reveal how the twisting of the C-N bond affects the neutral hydrolysis of amides. To do so, both concerted and stepwise mechanisms are studied and the results compared to the ones from the hydrolysis of an undistorted amide used as reference. In addition, an extra explicit water molecule that assists in the required proton-transfer processes is taken into account. Our results predict important rate accelerations of the neutral hydrolysis of amides when the C-N bond is highly twisted, the corresponding barrier relaxation depending on the specific reaction pathway and transition state involved. Moreover, our calculations strongly suggest a change in reaction mechanism with degree of amide bond twist, and clearly point to a concerted mechanism at neutral pH for the hydrolysis of highly twisted amides. In addition, the twisting of the amide bond also provokes a higher dependence on an auxiliary water molecule for the concerted mechanism, due to the orthogonality of the lone pair of the nitrogen and the carbonyl pi orbital. There is a direct implication of these findings for biological catalytic mechanism of peptide cleavage reactions that undergoes ground-state destabilization of the peptide.     

Probing the Catalytically Active Species in POM-Catalysed DNA-Model Hydrolysis**

Phosphoester hydrolysis is an important chemical step in DNA repair. One archetypal molecular model of phosphoesters is para-nitrophenylphosphate (pNPP). It has been shown previously that the presence of molecular metal oxide [Mo₇O₂₄]⁶⁻ may catalyse the hydrolysis of pNPP through the partial decomposition of polyoxomolybdate framework resulting in a [(PO₄)₂Mo₅O₁₅]⁶⁻ product. Real-time monitoring of the catalytic system using electrospray ionisation mass spectrometry (ESI-MS) provided a glance into the species present in the reaction mixture and identification of potential catalytic candidates. Following up on the obtained spectrometric data, Density Functional Theory (DFT) calculations were carried out to characterise the hypothetical intermediate [Mo₅O₁₅(pNPP)₂(H₂O)₆]⁶⁻ that would be required to form under the hypothesised transformation. Surprisingly, our results point to the dimeric [Mo₂O₈]⁴⁻ anion resulting from the decomposition of [Mo₇O₂₄]⁶⁻ as the active catalytic species involved in the hydrolysis of pNPP rather than the originally assumed {Mo₅O₁₅} species. A similar study was carried out involving the same species but substituting Mo by W. The mechanism involving W species showed a higher barrier and less stable products in agreement with the non-catalytic effect found in experimental results.     

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions     

Protein side chains facilitate Mg/Al exchange in model protein binding sites.

Among the most frequent protein binding sites served by Mg(II), we identify those which have higher affinity towards Al(III). We also estimate the free energies of metal exchange for all these binding sites taking into account solvent effects explicitly. The obtained results show that thermodynamically favored Mg(II)/Al(III) exchange reactions take place at a number of these metal binding sites, which could possibly be related to some dysfunctions of Mg(II)-dependent biological processes. Additionally, they shed light on the molecular basis of the toxicity of Al(III) in living organisms.     

Quantum Monte Carlo study of the ground state and low-lying excited states of the scandium dimer

A large set of electronic states of scandium dimer has been calculated using high-level theoretical methods such as quantum diffusion Monte Carlo (DMC), complete active space perturbation theory as implemented in GAMESS-US, coupled-cluster singles, doubles, and triples, and density functional theory (DFT). The 3 Sigma u and 5 Sigma u states are calculated to be close in energy in all cases, but whereas DFT predicts the 5 Sigma u state to be the ground state by 0.08 eV, DMC and CASPT2 calculations predict the 3 Sigma u to be more stable by 0.17 and 0.16 eV, respectively. The experimental data available are in agreement with the calculated frequencies and dissociation energies of both states, and therefore we conclude that the correct ground state of scandium dimer is the 3 Sigma u state, which breaks with the assumption of a 5 Sigma u ground state for scandium dimer, believed throughout the past decades.     

G2 study of triplet [H4, Si,P]+ potential energy surface: Mechanism for reaction of P+ (3P) with silane

A G2 search of the triplet [H₄, Si, P]⁺ potential energy surface (PES) was carried out, along with a study of a number of mechanisms for the reaction of the P⁺ (³P) ion with silane. The most stable isomer, which corresponds to the species resulting from transferring three hydrogen atoms from the silicon to the phosphorus atom, lies 67.3 kcal/mol below the reactants' level. The P⁺(SINGLE BOND)SiH₄ ion-molecule complex also has remarkable stability, 20.4 kcal/mol. Bond properties were calculated and are discussed for all the stable species found on the PES. Various exothermic reaction paths were also fully characterized. The abstractions of a hydrogen molecule and a hydrogen atom, yielding species with P(SINGLE BOND)Si bonds, have comparable kinetic hindrance, although release of molecular hydrogen was found to be more exothermic. Finally, hydrogen and/or charge transfer reactions between P⁺ (³P) and silane are also discussed. © 1997 by John Wiley & Sons, Inc.     

The Coulomb Hole of the Ne Atom

We analyze the Coulomb hole of Ne from highly-accurate CISD wave functions obtained from optimized even-tempered basis sets. Using a two-fold extrapolation procedure we obtain highly accurate results that recover 97 % of the correlation energy. We confirm the existence of a shoulder in the short-range region of the Coulomb hole of the Ne atom, which is due to an internal reorganization of the K-shell caused by electron correlation of the core electrons. The feature is very sensitive to the quality of the basis set in the core region and it is not exclusive to Ne, being also present in most of second-row atoms, thus confirming that it is due to K-shell correlation effects.