Dear Prof. Alan Shusterman,

I highly appreciate you= r time and support. your reply very much helped me to understand some of th= e critical aspects of ESP. Thank you for the help. Please let me ask one mo= re doubt. Is there any issues=20 related to the ESP plots of aromatic molecules (say, Benzene) having an=20 anionic or cationic substituent? As an example, Phosphonium-Benzene is a cationic system. Can we plot the ESPs of this system without=20 considering the counter ion (say, bromide)?

Thanking you

Dr. M. R. Ajaya= kumar

School of Physical Sciences

Jawaharlal Nehru Univ= ersity

New Delhi - 110 067

https://sites.google.com/site/mraj= ayakumarjnu/home

http://www.jnu.ac.in/Faculty/pritam/hom= e.html

On Sun, Mar 30, 2014 at 2:11 AM, Alan Sh= usterman alan%x%reed.edu = <owner-chem= istry*ccl.net> wrote:

Sent to CCL by: Alan Shusterman [alan],[reed.edu]
Dear Dr. Ajayakumar,

I believe your question 1) is asking about the difference between an electr= ostatic potential *isosurface* and an electrostatic potential *map*.

Because the electrostatic potential varies from one point in space to the n= ext, there are many ways to present information about potentials. An isosur= face shows points at which the potential is the same. A map shows how the p= otential varies across some arbitrarily chosen surface.

If this is confusing, consider this analogy. Temperature, like potential, v= aries with position. If we measure the temperatures around a pot of boiling= water, we could show our results by choosing one temperature value (say 30= C) 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 wo= uld 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 temperatu= re varies on this surface. There would be a range of temperatures on this s= urface 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 lo= cated 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 t= o use a surface where the electron density =3D 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 th= at are <=3D -1.24 are assigned a color at one extreme (often red) and po= tentials >=3D +1.24 are assigned a color at the other extreme (often dar= k blue). The extreme values, though, don't tell you how to interpret ot= her colors.

As for 3) it is usually a good idea to use the same potential-to-color mapp= ing 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 th= e 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 spa= n the full color spectrum, but the *more polar* DA system can still be iden= tified because it will have larger regions colored with the extreme colors = (large red and/or dark blue?).

4) I use Spartan (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 wrote:

Dear CCL subscribers,

I was confused for a long time about the representation/visualization of el= ectrostatic potential (ESP) surface (or mapping). In many litterateurs I sa= w the authors are describing the electron density differences of various mo= tifs 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 m= apping??
2) What is the significance of the scale of the surface plots (e.g. -1.24 t= o +1.24 eV)??
3) If I want to compare a set of similar D-A systems, whether I plot all th= e ESP mapped figures in a same scale?
4) Which are the best softwares (apart from GaussView) for ESP surface plot= s (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
http://www.jnu.ac.in/Faculty/pritam/home.htmlDear subscribe= rs,

--
Alan Shusterman
Chemistry Department
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202-8199
503-5= 17-7699
http://blogs.reed= .edu/alan/
"Nature doesn't make long speeches." Lao Tzu 23

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY*ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message
E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message http://www.ccl.net/chemistry/sub_u= nsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.= shtml
=A0 =A0 =A0ht= tp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/=