Water Molecule Adsorption on Protonated Dipeptides

Abstract

Equilibrium constants for the adsorption of the first water molecule on six protonated dipeptides (Gly-Gly+H(+), Gly-Ala+H(+), Ala-Gly+H(+), Ala-Ala+H(+), Pro-Gly+H(+), and Gly-Trp+H(+)) have been measured as a function of temperature, and DeltaH(o) and DeltaS(o) determined. Density functional theory calculations were performed for both the unsolvated peptides and the peptide water complexes at the B3LYP/6-311++G level. MP2/6-311++G** calculations were also carried out for Gly/Ala peptides. The calculations suggest that adsorption of a water molecule by these simple dipeptides is a complex process, both the unsolvated peptide and the peptide-water complexes have multiple conformations with similar free energies. Average DeltaH(o) and DeltaS(o) values derived from the calculations are in reasonable agreement with the experimental results. According to the calculations, the dominant water adsorption process involves a significant conformational change to accommodate a bridging water molecule. DeltaH(o) is diminished for Pro-Gly+H(+) mainly because the water interacts with a secondary amine, whereas for Gly-Trp+H(+), DeltaH(o) is significantly decreased by the loss of cation-pi interactions upon water adsorption. For unsolvated peptides the proton affinities of the N-terminus and the backbone carbonyl groups are known to be similar. Addition of a single water molecule causes a significant stabilization of the N-terminus protonation site.

Electron‐Capture‐Induced Dissociation of Microsolvated Di‐ and Tripeptide Monocations: Elucidation of Fragmentation Channels from Measurements of Negative Ions

“…[31] It should be noted that the second most stable [GA + H] + conformer lies 0.05 eV higher in electronic energy according to our calculations. These two bare ion structures correspond to the most stable structures found by Kohtani et al, [32] who explored the conformational space by means of molecular dynamics calculations followed by ab initio calculations. Their MP2 calculations [32] revealed that the structures are almost degenerate in electronic and free energies.…”

Bond dissociation of the dipeptide dialanine and its derivative alanine anhydride induced by low energy electrons

“…[5][6][7][8][9] These systems also allow high-accuracy ab initio calculations and are often considered as model systems for the study of more complex structures. In addition, the amino acid alanine has attracted attention due to its radiation dosimetric properties and has been formally accepted as a secondary standard for high-dose and transfer dosimetry.…”

The binding site dependence of binding energy in both metalated and protonated diglycine and triglycine peptides

“…The basis set superposition error (BSSE) [23] correction is taken into account also with 6-311++G ** basis set to estimate the error levels for all these BEs. Hybrid density functional theory (DFT/B3LYP) [24] calculations on these complexes are carried out thoroughly because the hybrid method of DFT can give very similar structural parameters compared with MP2, and the density functional vibrational frequencies and intensities are in excellent agreement with the experimental data for glycine and other amino acid systems [25], and also because of its successful treatments on the protonated and metalated oligoglycine systems [2,4,10].…”

“…Thus tridentate, bidentate or monodentate complexes can be obtained depending on the different metal-ion sizes, valences, binding sites, and the conformational flexibility of the peptide [10].…”

“…Peptides contain a series of active sites, such as their readily protonated amino-terminus nitrogens [2,4,10,11] and metalated [1] carbonyl oxygens. One of the most important applications of protonated peptides is in the mass spectrometry chemistry [11a], in which sequences of peptides and even proteins can be determined.…”