Feature Requests item #3284143, was opened at 2011-04-11 03:30
Message generated for change (Comment added) made by hansonr
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Category: Jmol extensions
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Granger Hermitage (ghermitage)
Assigned to: Bob Hanson (hansonr)
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.
----------------------------------------------------------------------
>Comment By: Bob Hanson (hansonr)
Date: 2011-05-01 19:01
Message:
correction:
version=12.1.45_dev
# new feature: NBO second-order data saved in modata:
# Var x = getProperty("auxiliaryInfo.models[2].moData.secondOrderData")
# show x
# >> x = [[69.0,115.0,1.2800001,0.044],[69.0,134.0,0.67,0.026],...[mo1,
mo2, E(2), f(i,j),...]
# where mo1 and mo2 are indexes into the MO list (Note that they are
floats, not integers.)
# and E(2) and f(i,j) are the E(2) value calculated by genNBO.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2011-05-01 18:51
Message:
version=12.1.45_dev
# new feature: NBO second-order data saved in modata:
# Var x = getProperty("auxiliaryInfo.models[2].moData.secondOrderData")
# show x
# >> x = [[69.0,115.0,1.2800001],[69.0,134.0,0.67],...[mo1, mo2, E(2)]
# where mo1 and mo2 are indexes into the MO list (Note that they are
floats, not integers.)
# and E(2) is the E(2) value calculated by genNBO.
Now, what we DO with those is another question....
----------------------------------------------------------------------
Comment By: Granger Hermitage (ghermitage)
Date: 2011-05-01 18:29
Message:
I am unaware of this being done elsewhere but it would be quite surprising
if it were not since interaction between pairs of orbitals is such a
central feature of some quantum analyses. Donor-acceptor interactions
(charge transfer) and steric pressure are examples of pairwise orbital
interactions, the first being unidirectional and the second being
bidirectional.
A colored arrow representing a vector would be a fine way of depicting
donor-acceptor interactions. It might be best to allow the orbitals
themselves not to be shown just the arrows as orbitals might obscure the
arrows. Allowing drawing of just the arrows would means that sense could be
made in a volume of numerous donor-acceptor interactions. The arrow would
be from and to nominal centers of orbitals. The arrow of the vector could
be of user-definable line width. When the mouse pointer was placed on the
arrow, the identities of both orbitals (NBO IDs and bond type details)
would be shown in text as would the E(2) and F(I,J) of the interaction.
For depiction of bidirectionally symmetric interactions, a line segment
rather than an arrow might be used.
The overlap would be the intersection of the visual representations of
PNBOs. However, colored arrows would have advantages over that.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2011-05-01 16:44
Message:
First question I would ask is this: Is this a totally novel idea, or do you
know of examples where programs do this?
Then: It seems to me we would need to depict two orbitals, and then
indicate by color (or a vector?) the strength and the direction of the
donor-->acceptor E(2) value.
"In the overlap" is a bit of a problem, I think. How would you define
that?
Bob
----------------------------------------------------------------------
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