Hey,
I've got a question which might be very simple. I was asked which interaction of amino acids is more energetically favorable. My problem begins with the what the definition of "energetically favorable" in molecular interactions is.
There were the following possibilities:
- Aspartic Acid and Lysin in water with a distance of 1.5 nm
- Aspartic Acid and Lysin in water with a distance of 1.0 nm
- Aspartic Acid and lysin in vacuum with a distance of 1.5 nm
I'm not sure about whether the screening effect of water plays any role. In addition these distances are quite long thus hydrogen bonding in water cannot play any role.. Maybe you have an idea. :)
Tanks a lot!
The "energetically more favorable" reaction (or molecular interaction) means that the deltaGo of the process is more negative. The molecular interaction thermodynamics strongly depends on local environment and positions of reactants relatively each other before and after the reaction. To answer your question would be a very hard job for theoreticians.
Not hard at all if you mean "lysine" (an amino acid, positively charged at pH7) rather than "lysin" (a family of proteins, this would make for an ambiguous question). Structure of lysine is here: https://en.wikipedia.org/wiki/Lysine
Yes. If you want to take the question on its own terms, you can just go straight in with q1q2/epsilon r^2. With epsilon=80epsilon_0 for water and 1 for vacuum. The question is very loosely posed, there is no mention of orientation of the sidechains or whether we are talking about COM-COM distance or charge-charge distance, so just go ahead and use the Coulomb formula.
Consider two interactions a and b.
Let us assume that
i) Externally energy needs to be supplied for the interaction a to take place
ii) energy is released during the occurrence of interaction b
Obviously interaction b is more probable than a or in other words, interaction b is energetically more favourable.
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