Many molecules can rotate internally around one or more of their bonds so that during a full 360 degrees rotation, they will change between unstable and relatively stable conformations. Ethane is the textbook example of a molecule exhibiting such behaviour: as one of its two methyl (CH3) groups rotates once around the central carbon-carbon bond, the molecule will alternate three times between an unstable eclipsed conformation and the preferred staggered conformation. This structural preference is usually attributed to steric effects; that is, while ethane rotates towards an eclipsed structure, the electrons in C-H bonds on the different C atoms are drawing closer to each other and therefore experience increased repulsion, introducing a rotation barrier that destabilizes the eclipsed structure. Stabilization of the staggered structure through rotation-induced weakening of the central C-C bond and hyperconjugation has been considered to be involved, but evaluation of the contributions of these effects to ethane's internal rotation barrier and conformational preference remains difficult. Here we report a series of ethane structure optimizations, where successive removal of different interactions indicates that ethane's staggered conformation is the result of preferential stabilization through hyperconjugation. Removal of hyperconjugation interactions yields the eclipsed structure as the preferred conformation, whereas repulsive forces, either present or absent, have no influence on the preference for a staggered conformation.
Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.
A flexing analysis of the ethane barrier energy in terms of structural (ΔEstruct), steric exchange (ΔEsteric), and hyperconjugative charge-transfer (ΔEdeloc) energy contributions has been carried out using natural bond orbitals. No evidence is found for the view that the ethane staggered equilibrium geometry or the C–C bond expansion that accompanies rotation results from steric exchange repulsion interactions. The analysis shows that ΔEstruct and ΔEdeloc have very different stereoelectronic dependencies, but that the ΔEsteric and ΔEdeloc dependencies are antagonistic. All of their contributions are strongly affected by the C–C bond expansion, with the result that the barrier mechanism cannot be understood without taking into account their different relaxation dependencies. Neglect of C–C expansion leaves the charge-transfer interactions paramount by subduing the steric and structural contributions. These interactions are found to be an important determinant for the expansion. The strong expansion dependence found for ΔEstruct is largely controlled by weakening of the C–C bond, and to a lesser extent by concomitant strengthening of the C–H bonds. Most of this dependence can be mimicked by C–C expansion in the absence of methyl torsion indicating that C–C bond weakening does not arise from the symmetry change accompanying ethane torsion.
We have applied molecular dynamics to investigate the structural properties and activity of recently synthesized amphiphilic polymethacrylate derivatives, designed to mimic the antimicrobial activity of natural peptides. The composition, molecular weight, and hydrophobicity (ratio of hydrophobic and cationic units) of these short copolymers can be modulated to achieve structural diversity, which is crucial in controlling the antimicrobial activity. We have carried out all-atom molecular dynamics to systematically investigate the conformations adopted by these copolymers in water and at the water-lipid interface as a function of sequence and the chemical nature of the monomers. For two sequences, we observe partial insertion into the bilayer. Formation of strong interactions between the lipid headgroups and the amine groups of the polymers assists in the initial association with the lipids. However, the primary driving force for the observed partial insertion appears to be the hydrophobic effect. Our results indicate sensitive dependence of the overall shape on the sequence, suggesting that experimentally observed changes in activity can be correlated with particular sequences, providing an avenue for rational design.
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