Subject: Re: Empirical solvation models

From: "Douglas A. Smith Ph.D." <[email-masked]>
Date: Thu, 14 Aug 1997 01:40:52 -0400

This is not a direct answer but may be of interest.

A few years ago we published a comparison of the use of molecular mechanics
(AMBER* force field) plus the GBSA solvation model versus the use of ab
initio plus Monte Carlo simulations for estimating conformational
equilibria in aqueous solution for four test cases:  1,2-ethanediol,
2-hydroxybenzoic acid, and both the neutral and protonated forms of
histamine.  The GBSA relative solvation free energies were consistently
smaller than the values obtained in the MC simulations when using the
charges from the AMBER* forceifield, and up to 30 percent underestimated
when using the charge sets from the MC simulation.  Comparisons were also
made to experimental data.  We ascribed the differences in the two
approaches as due to the application of torsional parameters and atomic
charges developed in the AMBER* forcie field for monofunctional polar
systems, while we were looking at difunctional molecules with the
possibility of intramolecular hydrogen bonding.

The reference:  P. I. Nagy, J. E. Bitar, D. A. Smith, J. Comput. Chem. 15,
1994, 1228-1240.

Doug Smith

At 02:24 PM 8/13/97 -0700, you wrote:
>
>Dear CCL netters
>
>Could someone points to me some empirical methods to 
>estimate free solvation energy of a molecule in
>aqueous solution? 
>
>There are many solvation models to calculate free
>solvation energy such as QM SCRF methods, AMSOL, PB,
>GBSA, MD, MC and etc.  What we would like to know is
>the performance of empirical methods, i.e., what are
>their standard errors over a large set of experimental 
>data or over other theoretical results, where an empirical
>approach will break down.  
>
>I will summarize the replies if there are enough
>interests.
>
>Thanks,
>
>Jian Wang,  Ph.D                             
>Department of Pharmaceutical Chemistry     Tel:  (415)-476-2597 (O)
>Box 0446, Room S-1019                            (415)-752-2256 (H)
>University of California                   Fax:  (415)-476-0688 (O)
>San Francisco, CA94143-0446                     
>U.S.A.                                     Email: [email-masked]
>
>
>-------This is added Automatically by the Software--------
>-- Original Sender Envelope Address: [email-masked]
>-- Original Sender From: Address: [email-masked]
>[email-masked]: Everybody | [email-masked]: Coordinator
>[email-masked]: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73
>Anon. ftp: www.ccl.net   | [email-masked] -- archive search
>             Web: http://www.ccl.net/chemistry.html 
>
>
>
--
Dr. Douglas A. Smith, President and CEO     |  voice: (814) 255-7859
The DASGroup, Inc.                          |    fax: (814) 255-3517
1732 Lyter Drive, 2nd Floor                 |  email: [email-masked]
Johnstown, PA 15905                         |    WWW: http://www.dasgroup.com

Contract R&D specialists in modeling, simulation, and synthesis for
chemistry, materials science, and biotechnology.