Consider the formation of a linear peptide (N-H to O=C) hydrogen bond where the

Question

Consider the formation of a linear peptide (N-H to O=C) hydrogen bond where the final N to O distance is 3A and the NH and CO bond lengths are 1A and 1.23A, respectively. Given the following atom charges qN = -0.3, qH = 0.3, qO = -0.6, and qC = 0.6, use the Coulomb potential (1389 qi qj / rij in kJ/mol when r is in A) to calculate the four distance dependent intermolecular interactions and thereby determine the total hydrogen bond strength in the gas phase. The dielectric constant of a protein interior is thought to be 4. What is the hydrogen bond strength in this environment?

Explanation / Answer

On H the net potential is

1389 * 0.3 * { -0.3 / 1 + -0.6 / 4 + 0.6 / 5.23}

= -139.71

Since dielectric constant is 4 we have to divide this

So net energy of the bond is (-139 .71 /4) kJ/mol

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