Polarization and 3D clean

User 8a8820633e

02-02-2006 14:46:35

Please excuse my ignorance, but i'm a physicist(all we seem to like is hydrogen!) becoming a chemist in 5 days...

When running the 3D clean, is it giving you the true 3D structure, or just something quick that looks nice? Sometimes, the optimize option will switch tetrahedral structures all around. So, which option is closer to the truth?

Also, when doing the polarizations, are the units Angstoms^3?

Finally, is it possible to extract the longitudinal and transverse components of the polarizations from the individual bond polarization numbers? I have retrieved the source article from 79 that gives the method that this program uses, and it doesn't seem to jive with the older Denbigh(1940) method of summing up the individual bond polarizations.

Any help in this would be great. Thank you Chemists!


User 65315e6b18

02-02-2006 16:26:00

Jpurdon wrote:


When running the 3D clean, is it giving you the true 3D structure, or just something quick that looks nice? Sometimes, the optimize option will switch tetrahedral structures all around. So, which option is closer to the truth?


Hi Joe,

The goal of 3D clean is finding the globally lowest energy 3D structure related to the given molecular toplogy in the framework of the Dreiding molecular mechanics forcefield. It is, however, possible, that the process cannot find the global minimum and also that the structure which is global minimum in the forcefield is far from the "truth". It should give reasonable results for most organic molecules.

The optimization should provide a local minimum started from the initial structure.

Best wishes,


ChemAxon 2136dd2f4b

02-02-2006 17:34:15

Dear Joe,

Yes, units are given in Angstoms^3.

Marvin has two different method for calculating polarizability.

1st method ., Miller, K. J.; Savchik, J. A.: J.Am.Chem.Soc., 1979, 101, 7206

2nd method ., Piet Th. van Duijnen.; Swart, M.: J.Phys.Chem. A, 1998, 102, 2399 (this article is freely available on the net)

Jensen, L.; Per-Olof Astrand.; Osted A.; Kongsted J.; Mikkelsen K.V.: J.Chem.Phys., 2002, 116, 4001 (this article is freely available on the net)

When you select "Take 3D geometry" option in Marvin than the 2nd method used for calculating polarizability.(Thole polarizability)

Test results are given here: http://www.chemaxon.com/marvin/chemaxon/marvin/help/Validations.html

Both methods are based on atomic fragments. (not bond fragments)

1st method calculates avarage molecular polarizability.

2nd method calculates avarage molecular polarizability form the principal polarizability componenets axx, ayy, and azz.

The polarizability components parallel/perpendicular to the bond axes connecting two atoms are given by Silberstein's equation. (See 2nd medhod).

Do you mean this on extraction longitudinal end transverse polarizability information?

Jozsi (chemist :-) )

User 8a8820633e

02-02-2006 18:26:28

Thanks for the quick responses.

So, the 2D polarization gives the atomic polarizabilities. If I have that information, as well as the bond length, is it possible to extract parallel and perpendicular components of individual bond polarizabilities within the molecule? The stuff i'm asked to do doesn't involve the entire molecular polarizability tensor. I'm supposed to find the bond polarizability components for each individual bond. So far, I can't seem to find a simple little formula on the net. Some places just say to average the two, but that doesn't seem to work. Thanks so much for your help.


ChemAxon 2136dd2f4b

02-02-2006 19:38:14

Dear Joe,

In this reference http://theochem.chem.rug.nl/publications/PDF/ft431.pdf

equations (5) and (6) are can be used for calculation parallel and perpendicular polarizability components of atoms.

Atomic polarizability values (in 2D) are calculated with the 1st method, and distances are available from Marvin or other source.

I don't know ,however,how parallel and perpendicular polarizability components are related with bond polarizability.

I remeber that in this book observed bond polarizability data are included.

Neil S. Isaacs, Physical Organic Chemistry, John Wiley & Sons, Inc., New York, 1987.


User 8a8820633e

02-02-2006 21:21:39

Silberstein's Equations blow up in my face because r is too small. Obviously, this problem is corrected as is shown in the papers, but it's a bunch of tensor notation that i'm not familiar with. I guess i'll have to get familiar with it.

about the components, I thought that the bond polarizability could be broken down into the perp and par components assuming an ellipsoid. Is that part completely wrong?

ChemAxon 2136dd2f4b

07-02-2006 14:16:56

Dear Joe,

Bond polarization method (BPM) for calculating molecular polarizability or other physical parameters (e.g. Raman spectrum) usually invokes parallel and perpendicular bond polarizability values. These two polarizability components obtained from experimental data or from quantum mechanical calculations.

Atom polarization method (APM) is not suitable for obtaining bond polarization data.

Please let me know if you have other opinion. Thanks.