Hey Jason
I am trying to calculate the reference energy for a hexane ring with a
-COOH side group. I get a value of ~-13 kcal/mol. I used the same partial
charge set for both the Thermodynamic Integration (TI) and CpHMD. I also
adjusted the value of partial charge on the beta carbon. I do not get a
change in protonation state. Previously, I tried Succinic Acid
(COOHCH2CH2COOH) and was able to use the reference energy from TI and got
50% protonation at pH = pKa.
Does the size of the model compound affect the protonation state change? If
the model compound is too big (say about 42 atoms), won't it not be able to
protonate/deprotonate? I am using a hexane ring with a -COOH group as this
in future is going to be a part of a polymeric chain. As a result, this is
the smallest model compound I can think of.
The EGB values in my simulation are pretty off compared to my del G value
NSTEP = 996000 TIME(PS) = 3992.000 TEMP(K) = 298.98 PRESS =
0.0
Etot = -255.6648 EKtot = 30.5979 EPtot =
-286.2626
BOND = 10.7378 ANGLE = 20.5709 DIHED =
28.0008
1-4 NB = 4.8937 1-4 EEL = -83.5682 VDWAALS =
-5.6856
EELEC = -2.1020 *EGB = -266.0849 *
Thank You
Rahul Ramesh
Masters Student
Department of Chemical Engineering
University of Michigan Ann Arbor
(+1 734-680-4453)
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Received on Fri Sep 18 2015 - 14:00:04 PDT
