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From: John Philo <"jphilo*NO SPAM12*"@earthlink.net>
Newsgroups: bionet.biophysics
Subject: Re: software to calculate molecular volume
Date: Mon, 06 Jul 1998 12:31:03 -0700
Organization: Alliance Protein Laboratories
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To: You Xing Qu <quyx@OLIGO.UTMB.EDU>

You Xing Qu wrote:
> 
> Dear all,
> 
> Does anyone know which free software can calculate the molecular volumes
> for small organic molecules like amino acids, urea, and sucrose?
> 
> Thanks in advance,
> 
> Youxing Qu
> 
> Dept. of Human Biol. Chem. & Genetics
> Univ. of Texas Medical Branch
> Galveston, TX 77555-1052
> E-mail: quyx@oligo.utmb.edu

It is not clear in what context you need to calculate volumes.  If you
are looking for "hydrated volume", i.e. how much volume a gram of a
given molecule occupies when it it dissolved in water, this quantity is
usually known as v-bar (a "v" with a bar over it), and is widely used in
the analytical ultracentrifugation field.  A large tabulation of values
for small molecules, proteins, and DNA can be found in H. Durchschlag,
'Thermodynamic Data for Biochemistry and Biotechnology', H.-J. Hinz,
ed., Springer-Verlag, New York, 1986, Chapter 3.  This article also will
lead you to references regarding calculating volumes by adding those for
individual groups (methyl, carbonyl, etc.)

My public domain program called SEDNTERP (a Windows application) has a
database containing v-bar values for amino acids, sugars, urea, and many
other compounds.  It's primarily intended for interpretation of
analytical ultracentrifugation data, but as part of that it will
calculate v-bar for any protein plus any of the small molecules in the
database.  It is not presently set up to calculate organic molecules
based on summing their constituent groups, but since you can add to the
database you could do that if you want.

It can be downloaded from the Ultracentrifugation software web site at
UTHSC in San Antonio,
http://bioc09.uthscsa.edu/auc
and I am sure that Professor Jim Lee's lab there at UTMB has it and uses
it.  Jim Lee would also surely have a copy of the Durschlag chapter,
which may not be available in your library.

I hope that helps.
 
John Philo, Alliance Protein Laboratories

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