Dear Prof. Alan Shusterman,
I highly appreciate your time and support. your reply very much helped
me to understand some of the critical aspects of ESP. Thank you for
the help. Please let me ask one more doubt. Is there any issues
related to the ESP plots of aromatic molecules (say, Benzene) having
an anionic or cationic substituent? As an example, Phosphonium-Benzene
is a cationic system. Can we plot the ESPs of this system without
considering the counter ion (say, bromide)?
Thanking you
Dr. M. R. Ajayakumar
School of Physical Sciences
Jawaharlal Nehru University
New Delhi - 110 067
https://sites.google.com/site/mrajayakumarjnu/home
http://www.jnu.ac.in/Faculty/pritam/home.html
On Sun, Mar 30, 2014 at 2:11 AM, Alan Shusterman alan%x%reed.edu
<http://reed.edu>;
<owner-chemistry[#]ccl.net
<mailto:owner-chemistry[#]ccl.net>> wrote:
Sent to CCL by: Alan Shusterman [alan],[reed.edu <http://reed.edu>;]
Dear Dr. Ajayakumar,
I believe your question 1) is asking about the difference between
an electrostatic potential *isosurface* and an electrostatic
potential *map*.
Because the electrostatic potential varies from one point in space
to the next, there are many ways to present information about
potentials. An isosurface shows points at which the potential is
the same. A map shows how the potential varies across some
arbitrarily chosen surface.
If this is confusing, consider this analogy. Temperature, like
potential, varies with position. If we measure the temperatures
around a pot of boiling water, we could show our results by
choosing one temperature value (say 30C) and showing all of the
points in space where our thermometer reads this temperature
(probably these would be points far away from the pot). This would
be a temperature isosurface. Or, we could define an arbitrary
surface (say the surface of the pot or the pot's lid), and ask how
the temperature varies on this surface. There would be a range of
temperatures on this surface and we would use a colored map to
show the variation in temperature.
Turning to question 2), there are several numbers that are used to
describe these two types of images.
For an isosurface, you need to say what value of the potential was
chosen. Returning to my analogy, a 60C isosurface would be much
more compact and located closer to the boiling water than a 30C
isosurface, so the temperature would need to be provided.
For a map, you need to say how the surface was chosen (a common
choice is to use a surface where the electron density = 0.002 au)
and then provide a legend for translating potentials into map
colors. Many potentials provide only the extreme values of the
legend and not the intermediate values. So when you see a range
like -1.24 to +1.24, this is saying that potentials that are <=
-1.24 are assigned a color at one extreme (often red) and
potentials >= +1.24 are assigned a color at the other extreme
(often dark blue). The extreme values, though, don't tell you how
to interpret other colors.
As for 3) it is usually a good idea to use the same
potential-to-color mapping for all of your maps. There is no
standard way to do this, but here are two choices to consider for
comparing two D-A systems.
Choice #1 - adjust the colors so that the full range of potentials
in the *more polar* DA system can be observed (that is, no
potentials fall outside the color range). Applying this same
mapping for the *less polar* DA system will create a map with
fewer colors and the colors will be dominated by the middle of the
potential-to-color legend (often green).
Choice #2 - adjust the colors so that the full range of potentials
in the *less polar* DA system can be observed. Now the colors on
both maps will span the full color spectrum, but the *more polar*
DA system can still be identified because it will have larger
regions colored with the extreme colors (large red and/or dark blue?).
4) I use Spartan (www.wavefun.com <http://www.wavefun.com>;). It's
very easy to learn and use. It is not free, but there are a
variety of packages with different prices
Best wishes,
Alan
On 3/28/14 11:57 PM, ajay mr mr.ajay.mr- -gmail.com
<http://gmail.com>;
wrote:
Dear CCL subscribers,
I was confused for a long time about the
representation/visualization of electrostatic potential (ESP)
surface (or mapping). In many litterateurs I saw the authors
are describing the electron density differences of various
motifs in an aromatic molecule, say, donor- acceptor (D-A)
kind of molecule. Using this surface plots they could easily
establish the electronic nature similar kind of systems (a
class of D-A molecules).
My doubts are,
1) Difference between Electrostatic potential and
electrostatic potential mapping??
2) What is the significance of the scale of the surface plots
(e.g. -1.24 to +1.24 eV)??
3) If I want to compare a set of similar D-A systems, whether
I plot all the ESP mapped figures in a same scale?
4) Which are the best softwares (apart from GaussView) for ESP
surface plots (preferably freewares)?
Looking for your kind support.
Thanking you,
Dr. M. R. Ajayakumar
School of Physical Sciences
Jawaharlal Nehru University
New Delhi - 110 067
https://sites.google.com/site/__mrajayakumarjnu/home
<https://sites.google.com/site/mrajayakumarjnu/home>;
http://www.jnu.ac.in/Faculty/__pritam/home.htmlDear
<http://www.jnu.ac.in/Faculty/pritam/home.htmlDear>;
subscribers,
--
Alan Shusterman
Chemistry Department
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202-8199
503-517-7699 <tel:503-517-7699>
http://blogs.reed.edu/alan/
"Nature doesn't make long speeches." Lao Tzu 23
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