AMBER: Opinion needed-Solvents

From: chaiann ng <>
Date: Thu, 01 Sep 2005 09:59:00 +0800

Dear Amber User:

I am using AMBER 8.0 to run explicit solvent MD by refering to the tutorial
website on amber homepage. I did some modification on the and
by increasing their steps and simulation times.

The solvents I am using are H2O, MEOH, DMSO and chloroform. My research aim
is to prove my molecule is changing its shape between hydrophobic and
hydrophilic enviroment. The input structure for antechamber(using bcc) for
each solvent is from DYANA software, which is using NMR constraints to
obtain DG

The results I got are as follow:

H2O Energy -32.99 +/- 2.65
MEOH Energy -23.93 +/- 2.42
DMSO Energy -45.14 +/- 1.20
CHCl3 Energy -46.75 +/- 6.35

The DMSO and CHCl3's energies are quite similar. In fact, I have a software
to calculate LogP of octanol to water of 3D structure, DMSO and CHCl3
structure gives 3.06 +/- 0.07 and 3.08 +/- 0.06 respectively. MEOH and H2O
structures give 2.8 +/- 0.09 and 2.58 +/- 0.05 respectively.

>From the results, DMSO are more hydrophobic than MEOH but the dielectric
constant of DMSO is higher than MEOH, and it is not any way closer to CHCl3.
My molecule has 4 C=O, 2 ester Oxygen and 1 OH.

I am thinking of DMSO is not a good solvent to stablize the molecule, not
like H2O and MEOH, where they can stabilize both C=O, O and OH, so DMSO is
pretty much acts like a hydrophobic solvent.
Any ideas or thought?

Thanks for your time.


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Received on Thu Sep 01 2005 - 03:53:01 PDT
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