Subject: Responses to question about UV calculation/CAChe vs Spartan

From: STEVE BAERTSCHI / 276-1388 / DROP 0724 <[email-masked]>
Date: Fri, 19 Jan 1996 10:29:26 -0500 (EST)

Dear Comp Chem List
   This is a summary of the four responses I received to my original post 
regarding the use of the CACHe and Spartan software systems for calculation
and prediction of UV spectra.

Steve Baertschi
[email-masked]
*************************
Reply number 1:
From: [email-masked]

Steve, Spartan does not use ZINDO to calculate UV spectra, rather it
uses singles and doubles CI in its semi-empirical module.  Both are
semi-empirical methods - ZINDO will appear as INDO/S in the literature.

I think Spartan's pretty easy to use...  All of the compute modules have
pretty similar interfaces (same style, mostly same contents), and this
carries over into the external packages which Spartan supports (such
as G9x).  Having written a bunch of Spartan, yeah, I'm pretty biased,
but the users were pretty/very happy with it.
 ...........
Joe
**********************************
Reply number 2:
From:[email-masked]
Hi Steve,

We are using a CAChe system, although I've never tried to predict UV spectra.
What I do know is that it is very easy to use, and that's true for all
modules. About the prediction of spectra, you might want to fire the
question to the CAChe user group, at

[email-masked]

I hope this is of any help!

Mirko

Mirko Kranenburg
Universiteit van Amsterdam
J.H. van 't Hoff Research Institute
Dept. of Inorganic Chemistry and Homogeneous Catalysis
Nieuwe Achtergracht 166
1018 WV Amsterdam
The Netherlands
tel. +31-20-5256417
fax. +31-20-5256456
e-mail: [email-masked]
************************
Reply number 3:
From: [email-masked]

Steve,
I can't comment on SPARTAN but I use the CAChe system quite often. I've only
calculated spectra a few times and really don't know how it compares to an
actual spectra but what I've done seems quite reasonable of course it doesn't
take into account solvent effects. You can calculate spectra with ZINDO or in
MOPAC with several force fields AM1, PM3,... The CAChe is great for non-experts
if you can use a Mac you can use CAChe, personally I find it to become a little
cumbersome in that it uses several different modules which load onto its
processor card which can lead to noticable delays. As an example I do a MOPAC
calculation, so build the molecule in the Editor, minimize in MOPAC so swap out
of the Editor and load MOPAC, when finished I want to look at the frontier
orbitals so swap out MOPAC load Tabulator and analyze the orbitals, to display
the results swap out of Tabulator and load Visulaizer. Cumbersome but easy to
use, it also gives very nice graphical output which is easy to understand. It's
a simple process to predict reactivity in this manner, you can also predict
IR's from MOPAC calculations.
Hope this helps,
David E. Reichert, Ph.D.
Mallinckrodt Inst. of Radiology
Div. Radiation Sciences
phone: (314)362-8461
fax: (314)362-9940
e-mail: [email-masked]
*************************
Reply number 4:
From: [email-masked]

Hi Steve,

I use the CAChe system quite a bit.  I am not as familiar with Spartan. 
Recently I've been calibrating some ZINDO based UV calculations, so I can
comment on your questions about CAChe ZINDO:

>Does the CAChe software do a good job of predicting real-world spectra?
>Does Spartan have a similar ZINDO module?  If it does, how do the two 
>user-inferfaces compare?

CAChe and Spartan both have very good user interfaces for setting up the
calculations you want, especially for:

>EASE OF USE for a non-expert!

CAChe also visualizes the results of a UV calculation nicely, with a
simulated spectrum that you can select absorbances from with a mouse click
and see the orbitals involved in that transition.  CAChe also includes
"Project Leader," a molecular spreadsheet that is well suited to developing
calibrations (as well as QSPR models), which I think you will want to do.

As you may or may not know, ZINDO is the INDO formalism for which parameters
(through the first row of transition metals) have been derived specifically
to reproduce experimental UV/Visible spectra, by performing a CI
(Configuration Interaction) calculation.  (It can also predict
fluorescence.)  So far as the accuracy, it does pretty well in the UV region
(within 20 nm or so in my experience), but is less reliable in the Visible
region.  In different studies, absorption maxima have been found to
correlate with the observed lambda max of: unsaturated aldehydes with R^2
0.998, benzenes with R^2 0.94, and a general sampling of organic compounds
with R^2 0.925.

I have two cautions about calculating absorbances of dyes (in the visible
region).  The first is that the error is greater, but is somewhat
systematic.  The thing to do is to do a series of calculations on molecules
similar to the one you're interested in to develop a calibration factor and
then apply that to your predicted absorbance.  Hydrazone dyes, for instance,
have a slope of 0.83, whereas anthraquinones have a slope of 2.3. (Masafumi
et. al. Dyes and Pigments, 1991, 17, 287-296.)

The other caution is that some absorbances are predicted to occur in the
visible region, but only with a negligible intensity.  Examining the
orbitals involved, the intensity is predicted to be near zero because the
orbitals are orthogonal.  In solution, however, (aside from the effect of
solvent shift) the presence of specific solvation molecules must break the
symmetry, because those absorbances are, in fact, observed.

One last remark on when you get to doing the calculations.  You will have
the option of several levels of CI to use.  In general, after the first
several levels, including additional levels of CI only increases the detail
of the low end (<200 nm) of the spectrum.

In response to your other interests:

>I am also interested in these parameters:  Reactivity of molecules (where is 
>the most nucleophilic site, the most electrophilic site, where would radical 
>attack occur, which hydrogen atom is easiest to abstract, how does the electron

>density map look at defined pH's, etc.), pKa estimation, IR prediction, 
>conformation, etc.

Both Spartan and CAChe have very good visualization, not only of orbitals,
but also of the surface of the molecule showing the relative susceptibility
to nucleophilic, electrophilic, etc. attack.  There will be a Midwest CAChe
users meeting in January that you may want to attend to get some training
and have a chance to see how well you can do what you want with the
software.  Send email to:

 [email-masked]

for more information, or to sign up.

I hope that helps.

EC
---
Ernest Chamot
Consultant in Computational Chemistry Applications
Chamot Laboratories, Inc.
530 E. Hillside Rd.
Naperville, Illinois 60540
[email-masked]

From: BAERTSCHI STEVE W             (MCVAX0::RC80281)

To:   VMS MAIL ADDRESSEE            (IN::"[email-masked]")