Adventures in Computational Chemistry

Returning to xleap again. The box I require this time has little tricky requirements. 1) The box should satisfy the molarity ratio for the solute: solvent. 2) Should be big enough that QMMM calculations can be carried out easily 3) combine sets of molecule-pairs which are interconvertible following a proton transfer. I have a pair of molecules say p(H)--i which can be converted to another set called P--I(H) following a proton transfer from p to i.So, p(H)--i <---> P-I(H) To fulfill condition (1), I initially created one molar box for p(H)--i called "PIN" and other box for P--I(H) called "PII" For condition (2) and (3), I created a bigger box with 7 PIN and 1 PII boxes. The idea is: after proton transfer from I to P, during the QMMM calculation, P--I(H) pair coming from "PII" should convert to p(H)--i pair like other pairs from "PIN" and the whole box should become homogeneous with 8 p(H)--i pairs. We begin with: PIN with