Literatur reference for "Dreiding energy"

While evaluating the Marvin software for teaching at the university, I searched for a literature reference for "Dreiding energy". As mentioned in the paper "Advanced Automatic Generation of 3D Molecular Structures. Gábor Imre et al.· 1st European Chemistry Congress, Budapest, Hungary, · 27-31 August, 2006." it is a force-field method, but there I didn't find a literature reference.


In your description of the plugins, there is also no reference, see screenshot096.png.





Where can I find a literature reference for "Dreiding energy" ?


Which formulas does Marvin use ?

HUWagner wrote:

While evaluating the Marvin software for teaching at the university, I searched for a literature reference for "Dreiding energy". As mentioned in the paper "Advanced Automatic Generation of 3D Molecular Structures. Gábor Imre et al.· 1st European Chemistry Congress, Budapest, Hungary, · 27-31 August, 2006." it is a force-field method, but there I didn't find a literature reference. In your description of the plugins, there is also no reference, see screenshot096.png. Where can I find a literature reference for "Dreiding energy" ? Which formulas does Marvin use ?

Hi,





The geometry plugin uses the 3D generation module (Clean3D),


(more information on it can be found at: http://www.chemaxon.com/conf/Advanced_automatic_generation_of_3D_molecular_structures.pdf ),


which contains a slightly modified implementation of the Dreiding forcefield as described here:


S. L. Mayo, B. D. Olafson, W. A. Goddard III., J. Phys. Chem., 1990, 94, 8897-8909

Hi ofarkas, thank you for your quick answer.


I have already read the paper of Gabor Imre et.al. So I have now to look for the paper in J. Phys. Chem., 1990, 94, 8897-8909 which we have in our library.

Hi,


I have got the paper mentioned above (J.Chem.Phys. 1990, 94, 8897-8909) and I have tried to reproduce some results given in the tables. There are no Dreiding Energy results (in kcal/mol) for ground state conformations in table IX "Errors in Calculating the Strutures for 76 Organic Molecules Using the DREIDING force field". There are only rms values. So I can only try to reproduce the "Conformational Energies" (table XII) and "Relative Energies" (table XIII).


The results are the following, given in the sequence


system, exptl, calcd paper, calcd using Marvin 5.0.0 (kcal/mol)


butane gauche/anti, 0.76, 0.75, 0.80


methyl ethyl ether gauche/anti, 1.50, 1.56, 1.64


cyclohexane twist-boat/chair, 5.70, 7.72, 7.85


decalin cis/trans, 1.00, 1.76, -4.61


In the first three examples the differences are not large, but there are differences.


But in the case of decalin there is a large difference.


In experiment the trans-configuration is more stable than the cis-configuration.





What's wrong ?

Hi,





Nothing is wrong. The default optimization criteria has been set to balance between accuracy and speed (this applies to the first three cases) which can be changed as options for ccxcalc or in the GUI (Tools/Conformation/Conformers). I suggest using very strict criteria for reproducing the data given in the literature. I do not know what was the problem in your case for decalin, as I could reproduce the energy difference correctly.


Here are my numbers (using Marvin 5.0):


butane gauche/anti, 0.75


methyl ethyl ether gauche/anti, 1.55


cyclohexane twist-boat/chair, 7.72


decalin cis/trans, 1.76


Please, also find the attached structure files.





Best wishes,





Ödön

HUWagner wrote:

Hi, I have got the paper mentioned above (J.Chem.Phys. 1990, 94, 8897-8909) and I have tried to reproduce some results given in the tables. There are no Dreiding Energy results (in kcal/mol) for ground state conformations in table IX "Errors in Calculating the Strutures for 76 Organic Molecules Using the DREIDING force field". There are only rms values. So I can only try to reproduce the "Conformational Energies" (table XII) and "Relative Energies" (table XIII). The results are the following, given in the sequence system, exptl, calcd paper, calcd using Marvin 5.0.0 (kcal/mol) butane gauche/anti, 0.76, 0.75, 0.80 methyl ethyl ether gauche/anti, 1.50, 1.56, 1.64 cyclohexane twist-boat/chair, 5.70, 7.72, 7.85 decalin cis/trans, 1.00, 1.76, -4.61 In the first three examples the differences are not large, but there are differences. But in the case of decalin there is a large difference. In experiment the trans-configuration is more stable than the cis-configuration. What's wrong ?

Hi,





thank you for your quick and detailed answer.


I will further evaluate these calculations and then post the result.





Regards, Hans-Ulrich

Hi,


I can now reproduce the Dreiding Energy results to the fifth decimal digit ! The cis/trans decalin problem was a mistake of *my* input. Until now I used the "very strict" criteria only for "geometry" calculations, but of course the "conformation" tool uses the same procedure. Thank you for your instruction. I will inform my students.


It was a very good information to get the sdf-files. Now I am very interested in the diphenyl derivative ACTHBZ of the basic paper mentioned above. I have problems with diphenyl derivatives.





(BTW a little joke: My Linux KDE platform is recognising the sdf-files as "StarOffice: Mathematisches Dokument". Clicking on it opens the file with OpenOffice Writer as a plain text document and I can read it ;-)





Thank you, once more.


Regards, Hans-Ulrich

Hi Ödön,





can you please produce a sdf-file for the diphenyl example ACTHBZ (page 8902) found in the "DREIDING-paper" (S. L. Mayo, B. D. Olafson, W. A. Goddard III., J. Phys. Chem., 1990, 94, 8897-8909). It would be very helpful, to have a comparison to my examples.





Regards, Hans-Ulrich

Hi,


I found the "DREIDING-paper" (S. L. Mayo, B. D. Olafson, W. A. Goddard III., J. Phys. Chem., 1990, 94, 8897-8909) in the internet:





http://www.wag.caltech.edu/publications/sup/pdf/256.pdf





Regards, Hans-Ulrich

HUWagner wrote:

Hi Ödön, can you please produce a sdf-file for the diphenyl example ACTHBZ (page 8902) found in the "DREIDING-paper" (S. L. Mayo, B. D. Olafson, W. A. Goddard III., J. Phys. Chem., 1990, 94, 8897-8909). It would be very helpful, to have a comparison to my examples. Regards, Hans-Ulrich

Hi Ödön,


thank you for your quick help.


Regards, Hans-Ulrich