On the metastability of doubly charged homonuclear diatomics.

Generalized valence bond (GVB) and spin-coupled (SC) calculations were used in conjunction with the generalized product function energy partitioning (GPF-EP) method to describe the origin of metastability in doubly charged homonuclear dications. A model to describe the formation of metastable potential wells based on interference and quasi-classical effects is presented. The GPF-EP picture of dications is the result of polarization-aided strong covalent bonding surpassing Coulomb electrostatic repulsion. Important differences in the quasi-classical density profiles of He22+ and Ne22+ reveal the underlying mechanism that could lead to bound or unbound states. Finally, the nature of the chemical bond of N22+, O22+, and F22+ is described. The results suggest that the ground states of the mentioned dications are bounded and that the depth of the potential wells of these exotic species is related to the interference effect, in the same way as in previously studied neutral molecules.

The Nature of the Singlet and Triplet States of Cyclobutadiene as Revealed by Quantum Interference.

The generalized product function energy partitioning (GPF-EP) method is applied to the description of the cyclobutadiene molecule. The GPF wave function was built to reproduce generalized valence bond (GVB) and spin-coupled (SC) wave functions. The influence of quasiclassical and quantum interference contributions to each chemical bond of the system are analyzed along the automerization reaction coordinate for the lowest singlet and triplet states. The results show that the interference effect on the π space reduces the electronic energy of the singlet cyclobutadiene relative to the second-order Jahn-Teller distortion, which takes the molecule from a D4h to a D2h structure. Our results also suggest that the π space of the (1) B1g state of the square cyclobutadiene is composed of a weak four center-four electron bond, whereas the (3) A2g state has a four center-two electron π bond. Finally, we also show that, although strain effects are nonnegligible, the thermodynamics of the main decomposition pathway of cyclobutadiene in the gas phase is dominated by the π space interference.

Membrane-disruptive properties of the bioinsecticide Jaburetox-2Ec: implications to the mechanism of the action of insecticidal peptides derived from ureases.

Jaburetox-2Ec, a recombinant peptide derived from an urease isoform (JBURE-II), displays high insecticidal activity against important pests such as Spodoptera frugiperda and Dysdercus peruvianus. Although the molecular mechanism of action of ureases-derived peptides remains unclear, previous ab initio data suggest the presence of structural motifs in Jaburetox-2Ec with characteristics similar to those found in a class of pore-forming peptides. Here, we investigated the molecular aspects of the interaction between Jaburetox-2Ec and large unilamellar vesicles. Jaburetox-2Ec displays membrane-disruptive ability on acidic lipid bilayers and this effect is greatly influenced by peptide aggregation. Corroborating with this finding, molecular modeling studies revealed that Jaburetox-2Ec might adopt a well-defined beta-hairpin conformation similar to those found in antimicrobial peptides with membrane disruption properties. In addition, molecular dynamics simulations suggest that the protein is able to anchor at a polar/non-polar interface. In the light of these findings, for the first time it was possible to point out some evidence that the peptide Jaburetox-2Ec interacting with lipid vesicles promotes membrane permeabilization.

A molecular dynamics study of the correlations between solvent-accessible surface, molecular volume, and folding state.

We analyzed the correlations between molecular volume, solvent-accessible surface, and folding state (secondary structure content) for unfolded conformers of alpha (holo- and apomyoglobin) and beta (retinal-binding protein) proteins and a small water-soluble alanine-rich alpha-helical peptide. Conformers with different degrees of folding were obtained using molecular dynamics at constant temperature and pressure with implicit solvent (dielectric constant adjustment) for all four systems and with explicit solvent for the single helix peptide. Our results support the view that unfolded conformations are not necessary extended, that volume variation is not a good indication of folding state and that the simple model of water penetrating the interior of the protein does not explain the increase in volume upon unfolding.

On the generalized valence bond description of the anomeric and exo-anomeric effects: an ab initio conformational study of 2-methoxytetrahydropyran.

An ab initio conformational study of the alpha- and beta-glycosidic C1-O1 bonds has been carried out on the axial and equatorial forms of 2-methoxytetrahydropyran (2-MTHP) at the HF/6-31G(d,p) and GVB-PP/6-31G(d,p) levels of calculation. Six conformers of 2-MTHP were fully optimized at both levels. The calculations have shown that the conformer containing the (+sc) orientation around the axial C1-O1 bond is the most stable one and is favored over that bearing the (-sc) arrangement about the equatorial C1-O1 bond by 1.39 (HF) and 1.52 (GVB-PP)kcal/mol. The potential energy surfaces for rotating about the axial and equatorial C1-O1 bonds were constructed at the HF and GVB-PP levels. For each form of 2-MTHP the HF and GVB-PP potential curves exhibit similar profiles. This shows that both methods provide similar descriptions for the position of the conformational minima and for the values and location of the rotational barriers. In addition to the conformational study, a discussion concerning the nature of the chemical bond in acetal fragments and the origin of the anomeric and exo-anomeric effects is presented in terms of optimized non-orthogonal GVB orbitals of 2-MTHP. The intramolecular factors that respond for the order of stability and conformational changes in bond lengths of the conformers of 2-MTHP are examined in light of the GVB description. The problems associated with the use of the NBOs (natural bond orbitals) to analyze chemical bonding in the acetal fragments are discussed, and the choice for the GVB-PP description is justified.

Ab initio conformational maps for disaccharides in gas phase and aqueous solution.

Ab initio conformational maps for beta-lactose in both the gas phase and in aqueous solution have been constructed at the HF/6-31G(d,p) level of calculation. The results of the gas-phase ab initio calculations allow us to conclude that a rigid conformational map is able to predict the regions of the minima in the potential energy surface of beta-lactose, in full agreement with those found in the relaxed conformational map. The solvation effects do not give rise to any new local minimum in the potential energy surface of beta-lactose, but just change the relative Boltzmann populations of the conformers found in the gas-phase calculations. The values obtained for heteronuclear spin coupling constant (3J(H,C)), using the seven most stable conformers in solution are in good agreement with the available experimental values. This is a good indication that ab initio rigid conformational maps can be reliably used to sort the most stable conformers of beta-lactose.