OK, that's a great start, Reinhold. Now I need a volunteer to make this their legacy contribution to Jmol. Any takers?
Reinhold Stoermann wrote: > A few weeks ago I asked you about the possibility to show "molecular > lipohilic(ity) potential" (MLP) with jmol, as can be done with Chime. > > You said that it would be important to know *h*o*w* this potential > can be calculated, how this is done in Chime or better how this can be > done correctly. > > Although I cannot give you the exact answer now, I found some cited > literature on this subject. Unfortunately I have no access to the > relevant literature (these journals are not available at the > University of Bremen), but maybe you have. > > Concept of MLP can be found here: > > F. Croizet, M.H. Langlois, J.P. Dubost, P. Braquet, E. Audry, > Ph.Dallet, J.C. Colleter, J.Mol.Graphics., 8 (1990) 153. > > Gaillard, P., Carrupt, P.A., Testa, B. and Boudon, A., J.Comput.Aided > Mol.Des. 8, 83-96 (1994) > > Audry, E.; Dubost, J. P.; Colleter, J. C.; Dallet, P. A new approach > to structure-activity relations: the "molecular lipophilicity > potential". Eur. J. Med. Chem. 1986, 21, 71-72. > > Fauchere, J. L.; Quarendon, P.; Kaetterer, L. Estimating and > representing hydrophobicity potential. J. Mol. Graphics 1988, 6, 203-206. > > The site > > http://bip.weizmann.ac.il/course/prog2/graphics/chimescript2.html > (there find: "set mep|mlp function") > > give some formulas of calculating the MLP for a point on a molecular > surface, which seem have been used in Chime. Unfortunately it is not > not stated where to get the ("f = Lipophilic value for atom i") but > possibly that is provided in the above mentioned literature. > > A somewhat newer article is cited here: > > Theoretical derivation of heuristic *molecular* *lipophilicity* > *potential*: a quantum chemical description for *molecular* solvation. > <http://lib.bioinfo.pl/pmid:15807498>[My paper] Qishi Du > <http://lib.bioinfo.pl/auth:Du,Q> , Peng-Jun Liu > <http://lib.bioinfo.pl/auth:Liu,P> , Paul G Mezey > <http://lib.bioinfo.pl/auth:Mezey,PG> > > We present the theoretical derivation of a heuristic *molecular* > *lipophilicity* *potential* (HMLP), which gives a structure-based and > quantum chemical description of an important aspect of *molecular* > solvation. The quantum mechanical electrostatic *potential* (ESP) V(r) > on a formal *molecular* surface is calculated, and then the > *molecular* *lipophilicity* *potential* L(r) is constructed by > comparing the local electron density with the ESP on the surrounding > atoms using a screening function. The screening function is derived > from statistical mechanical theory treating the polar solvent > molecules as dipoles. HMLP is able to describe the main interactions > of solute molecules with polar and nonpolar solvent molecules. HMLP is > a unified *lipophilicity* and hydrophilicity *potential*: its positive > values represent *lipophilicity*, and its negative values represent > hydrophilicity. In this paper, several examples show that HMLP gives > more reliable descriptions for the *molecular* solvation than some > other methods, such as atomic partial charges and the empirical > *lipophilicity* *potential*. > Anal Biochem. 2005 Feb 15;337 (2):262-70 15691506 > > So I hope you can eventually find a way to implement the MLP surface > in Jmol sometime in the not so far away future. That would be great. > > Greetings from > Dr. Reinhold Störmann > Bioorganic Chemistry > Center for Environmental Research & Technology (UFT) > Leobener Str. > D-28359 Bremen > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
