Peptide group dipole moment

As an example, the charged phosphate group on phosphatidylethanol-amine, for example, can interact with the hydrocarbon (CH2) chain of an amino acid—for example, valine—in a peptide. A similar situation would hold in the example to the right for interaction of the hydrocarbon unit in a peptide chain. In both instances the groups with permanent dipole moments can induce a temporary dipole moment in an adjacent molecule. These interactions, however, are very weak and act only at very short distances thus the polarization energies may be of the order of 0.002-0.004 kcal/mol at a distance of 5 A. 

The two-exciton manifold consists of two types of doubly excited vibrational states. The first are overtones (local), where a single bond is doubly excited. The other are collective (nonlocal), where two bonds are simultaneously excited (43,50). We denote the former OTE (overtone two-excitation) and the latter CTE (collective two-excitation). A pentapeptide has 5 OTE and 10 CTE. The two-exciton energies are determined by the parameters gn in the Hamiltonian [Equation (17)], which in turn depend on the peptide group energies G , the anharmonicity An, and dipole moment ratio Kn, n = l,...,5. We set them equal for all CO units... 

The polypeptide backbone of a protein [ Figure 12.20(a) ] consists of a repeated sequence of three atoms — the amide nitrogen (N ), the a-carbon (Ca), and the carbonyl carbon (C ), where i is the number of the residue starting from the amino end (remember the order of words in amino acid ). The repeat distance for peptide units in a trans conformation is approximately 3.8 A. The peptide group has a permanent dipole moment with the negative charge on the carbonyl oxygen atom. The peptide bond is not chemically very reactive, and protons are lost or added onh at extremes in pH. 

FIGURE 12.23. Planarity of the amide group. Two resonance forms of the peptide group are shown. The possibility of a double bond between C and N argues for restriction of rotation about this bond. The charged resonance hybrid gives rise to a dipole moment. 

Groups with a strong dipole moment also become hydrated. A case in point is the peptide bonds in proteins. 

This causes the peptide bond to be flat rotation about the CO—NH axis is not possible. The bond is in the trans configuration, which is far more stable than the cis one. The peptide bond also has a significant dipole moment of 3.5 Debye units this implies that it tends to be hydrated. The H of the —NH group can act as a donor, the =0 as a hydrogen acceptor in forming hydrogen bonds. 

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