Feature Requests item #3284143, was opened at 2011-04-11 18:00
Message generated for change (Tracker Item Submitted) made by ghermitage
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3284143&group_id=23629

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: Jmol extensions
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Granger Hermitage (ghermitage)
Assigned to: Nicolas (nicove)
Summary: depict donor-acceptor energies

Initial Comment:
The energy of stabilization of a donor-acceptor interaction is given as the 
E(2) value in this NBO report:

 SECOND ORDER PERTURBATION THEORY ANALYSIS OF FOCK MATRIX IN NBO BASIS

     Threshold for printing:   0.01 kcal/mol
                                                                                
E(2)  E(j)-E(i) F(i,j)
      Donor NBO (i)              Acceptor NBO (j)       kcal/mol   a.u.    a.u. 
 ===============================================================================

 within unit  1
     1. BD ( 1) C 1- C 2       204. RY*( 1) O 3                1.86    1.86     
0.053
     1. BD ( 1) C 1- C 2     1308. BD*( 1) N 7- C 8         5.31    1.46    
0.079
 152. LP  ( 1) O20           1237. BD*( 1) N69- H74       8.25    1.68    0.105
 140. CR ( 1) C80           1110. RY*( 3) C83                1.32  13.77    
0.120

It would be really nice if the E(2) value could be depicted graphically. A 
point in a color spectrum corresponding to the value could appear in the 
overlap of the donor PNBO and the acceptor PNBO. PNBOs are better for showing 
overlap than the NBOs. Donor acceptor interactions are directional, so a 
particular interaction is specified by an ordered pair of NBO IDs, but there is 
no conflict with an interaction in the reverse direction since in how these 
things work there won't be one. If the mouse pointer was placed on one of the 
overlaps, the numeric E(2) value associated with the color would be shown. The 
ability to show the overlaps from a particular donor to all its acceptors and 
show overlaps to a particular acceptor from all its donors is highly desirable. 
A threshold of E(2) value would further subset which overlaps were shown.

Also, it is desirable that the pairwise steric exchange energies (another NBO 
report) receive a similar treatment. Both directions exist in this case, but 
the value should be the same in both cases so the same approach (showing a 
color in the PNBO overlap) would work.

As it stands these values have to be looked up from a long text report and a 
graphical depiction would be so much more convenient. 


----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3284143&group_id=23629

------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
Jmol-developers mailing list
Jmol-developers@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-developers

Reply via email to