When we model proteins on the computer, we must assign a partial charge to each of the non-ionized atoms. Let's consider the hydrogen bond between a carbonyl oxygen with a partial charge of -0.5 and an amino hydrogen with a partial charge of +0.3. The distance between these atoms is typically about 2A. Calculate the electrostatic energy for this interaction, using a dielectric constant of 3. Express your answer in kcal/mol.
Assigning partial charges is a difficult task, for reasons that will become apparent later in the course. Suppose we made errors in the above assignments and assigned partial charges of -0.3 for the oxygen atom and _0.2 for the hydrogen atom. Calculate the electrostatic energy for this interaction. The difference between this value and your answer to problem 3 is the size of the error we have made. Comment on this error. In particular, is it large enough that we need to worry about it?
There is always some uncertainty in the value of the dielectric constant, too. Using the charge values in problem 3, calculate the energy if we had used a dielectric constant of 2. once again, is the error large enough that we should be concerned, or not?
First let's find the conversion factor between joules and kcal/mol:
The energy between two charges separated by distance r in a medium with dielectric constant e is given by:
Where k is Coulomb's constant.
In our case:
The electrostatic energy of this bond is -8.3 kcal/mol. The negative sign indicates that we need to invest ...
The expert examines electrostatic energy of non-ionized atoms.