Water peptide interaction energy

Zhang, D. W, Chen, X. H., and Zhang, J. Z. H. (2003). Molecular caps for full quantum mechanical computation of peptide-water interaction energy, Joumai of Computationai Chemistry 24,15, pp. 1846-1852. 

Many other interaction energies come from the electromagnetic frequency spectrum. They can come from outside of the ultraviolet, visible, and infrared frequency ranges. All that is required is an element of the model protein in water that is able to take up the energy. The dipole moment of the peptide group with its positive end at the NH and its negative end at the oxygen of the CO provides one site of inter-... 

In the unfolded state, the peptide chain and its R groups interact with solvent water, and any measurement of the free energy change upon folding must consider contributions to the enthalpy change (AH) and the entropy change (A.S) both for the polypeptide chain and for the solvent ... 

This type of simulation has been often used to study peptide-phospholipid interactions. In these simulations, the hydrophobic term has usually been derived from hydrophobidty scales of amino acid side chains, but more detailed descriptions based on the transfer energy from water to a hydrophobic environment and the accessible molecular surface have also been developed [1, 2], The hydrophobic contribution then takes the following form ... 

Here I think some remarks on hydrophobic interactions ( l) would be appropriate. It is generally accepted now, that hydrophobic interactions are a contributing factor to protein behaviour and esp. to the formation of the secondary structure, e.g. helix. This means, that as shown in Figure 1 hydrophobic residues of the amino acids in a peptide are driven together by clusters of water molecules and so the secondary structure of a peptide or protein is formed. For the transfer from the helical to the stretched form, Tanford (2) found that the transfer free energy of the total protein results from the sum of the contributions of the single amino acid residues. 

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