Simulations of nanocylinders self-assembled from cyclic ß-tripeptides.

This paper examines the self-assembly of cyclic ß-tripeptides using density functional theory. On the basis of literature precedents, these cyclic peptides were expected to self-assemble into cylindrical structures by stacking through backbone-backbone hydrogen bonding. Our calculations show that such stacking is energetically favorable, that the association energy per cyclic peptide decreases (becomes more favorable), and that the overall macrodipole moment of the cylindrical assembly increases with the number of stacked rings, for up to eight rings. For a structure in which two peptide ring units are joined through a single side chain-side chain covalent linker, the association energy between the two rings is favorable, albeit less so than for the unlinked rings. Significantly, the association energy in the dimers is only weakly dependent on the length (above a certain minimum) and conformation of the covalent linkers. Finally, as a plausible route for controlling assembly/disassembly of nanocylinders, we show that, for a pair of rings, each bearing a single amino-functionalized side chain, protonation of the amino group results in a strongly positive (unfavorable) association energy between the two rings.

Exploring Relative Thermodynamic Stabilities of Formic Acid and Formamide Dimers - Role of Low-Frequency Hydrogen-Bond Vibrations.

The low-frequency fundamentals together with the high-frequency modes, responsible for hydrogen bonding (OH/NH stretching modes), were analyzed to correlate the intensities with the hydrogen-bond strengths/binding energies of the formic acid and formamide dimers using Møller-Plesset second-order perturbation (MP2) and coupled cluster computations with explicit anharmonicity corrections. Linear correlations were observed for both the formic acid and formamide dimers, and as consequence of such correlation an additive properties of binding energies with respect to the local hydrogen-bond energies of fragments involved (for these dimers) has been proposed. It has been further observed that (i) the nature of their six low-frequency fundamentals are very similar, and (ii) the in-plane bending and stretch-bend fundamentals of different dimers of these two species (depending on the dimer structure), in this low-frequency region, modulate their strength of hydrogen-bond/binding hence their relative stability order. These results were further verified against the results from Gaussian-G4-MP2 (G4MP2), Gaussian-G2-MP2 (G2MP2), and complete basis set (CBS-QB3) methods of high accuracy energy calculations.