From owner-chemistry@ccl.net Tue Apr 3 05:34:02 2007
From: "Jens Spanget-Larsen spanget[#]ruc.dk" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: semiempirical single & double excitations?
Message-Id: <-33953-070403050408-342-++WUUbFq+TBCYyXTIq1BFg#%#server.ccl.net>
X-Original-From: Jens Spanget-Larsen <spanget.:.ruc.dk>
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Date: Tue, 03 Apr 2007 11:03:48 +0200
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Sent to CCL by: Jens Spanget-Larsen [spanget(0)ruc.dk]
Dear CCL!
I just wish to emphasize that a number of UV-VIS chromophores cannot be
correctly described without the inclusion of multiply excited
configurations in the CI procedure. Within the framework of the
classical PPP pi-electron model, Michl and his coworkers developed the
SECI-1 and SECI-2 procedures, with inclusion of systematic and
well-defined selections of doubly excited configurations [1]. One of the
early all-valence electrons CI-procedures with inclusion of doubly
excited configurations was developed by H. Baumann, and his computer
program (CNDUV99) was made available through QCPE [2]. A reparameterized
version of Baumann's procedure was applied by Spanget-Larsen and Gleiter
[3] to the prediction of electronic transitions for a variety of
conjugated hydrocarbons. The investigation included 'normal' compounds
as well compounds with low-lying states depending on the inclusion of
doubly-excited configurations in the CI expansion. In particular, the S2
state of pleiadene and the S3 state of azuleno{1,2,3-cd)phenalene were
predicted to be of 67% and 31% doubly excited character, respectively.
It is important to realize that for these and other species with low
HOMO-LUMO excitation energy, a CI-model without the inclusion of
doubly-excited configurations does not qualitatively explain the
observed low-energy transitions.
Jens >--<
[1] J. W. Downing, J. Michl, P. Jorgensen, E. W. Thulstrup, Theor. Chim.
Acta 32, 203 (1974)
[2] H. Baumann, QCPE 10, 333 (1977)
[3] J. Spanget-Larsen, R. Gleiter, Helv. Chim. Acta 61, 2999 (1978)
------------------------------------------------------
JENS SPANGET-LARSEN Office: +45 4674 2710
Dept. of Science (18.1) Fax: +45 4674 3011
Roskilde University Mobile: +45 2320 6246
P.O.Box 260 E-Mail: spanget|ruc.dk
DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget
------------------------------------------------------
From owner-chemistry@ccl.net Tue Apr 3 06:51:01 2007
From: "Marianna Fanti marianna.fanti%x%unibo.it" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: SUMMARY: semiempirical single & double excitations
Message-Id: <-33954-070403061226-22147-OmW3bCUamkvS2Pm5JOKwkA{}server.ccl.net>
X-Original-From: Marianna Fanti <marianna.fanti#,#unibo.it>
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Date: Tue, 03 Apr 2007 10:32:01 +0200
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Sent to CCL by: Marianna Fanti [marianna.fanti%unibo.it]
Hello!
Few days ago I posted the following question:
> I'm looking for a semiempirical package with spectroscopic parametrization
(INDO/S for instance) able to handle single AND double excitations when doing
the CI.
>
> Is there any around? It seems that all the available packages are limited to
single excitations (CIS).
>
> I will summarize.
Thanks to everybody!
Here is the summary of the answers I received, but first a short comment.
Yes of course, CISD has many limitations, but I agree with John McKelvey
answer (of course... since I posted the question.. :D ).
===
Pierre Archirel pierre.archirel=lcp.u-psud.fr wrote:
I think that double excitations are contradictory with the semi-empirical
philosophy:
1- the basic ansatz is that the wave function is a single determinant, the
hamiltonian is parametrised so as to yield exact experimental values for the
ground state of a list of molecules.
2- this means that electron correlation implicitely lies in the parametrisation
and that CI of the doubles would be redundant. I am sure that this CID would
lower the energy, but I do not see any ground for doing it. This is also true
for excited states.
3- I conclude that the only way of performing a CI of the doubles in the right
way would be to reoptimise the paramaters in this frame. Maybe it is what you
want to do.
===
John McKelvey jmmckel%a%gmail.com wrote:
ORCA [free] should be able to do this. Also, since INDO/S was parameterized
using CIS, including doubles will likely blue shift transitions.
====
Sent to CCL by: "Greg Pearl" [greg.pearl(a)acdlabs.com]
The ZINDO code developed by Mike Zerner had that functionality.
Not sure how you can get that code these days but would start by
contacting
The Quantum Theory project at University of Florida
www.qtp.ufl.edu
====
John McKelvey jmmckel%a%gmail.com wrote:
From a purist point of view I agree with Pierre.
However, Zerner, the major player in the INDO/S domain, was able to explain a
lot of chemistry doing things with INDO/S beyond CIS. [ZINDO has the capability
to do CIS, CISD, CISDT, CISDTQ, ..etc.] In fact there are times where CISD is
necessary to get the orbital description of states correct, even though the
energies may be incorrect. Further, there are occasions where getting the
energies correct _requires_ CISD within INDO/S, as in describing solute-solvent
dispersion energies where a double excitation is composed of a single excitation
in the solute coupled with a single excitation in the solvent.
My $0.02.
====
Sent to CCL by: Frank Neese [neese^-^thch.uni-bonn.de]
Dear Marianna,
i just wanted to briefly follow up on what John McKelvey posted to the list.
Indeed, you can "torture" the MRCI module of the ORCA program to do a multiroot
CISD calculation. It is not really what it was made for but it is possible.
Below you find an input for H2CO:
#
# CISD calculation with ZINDO/S
#
! ZINDO/S TightSCF
%mrci citype mrci
tsel 0
solver diag
newblock 1 *
nroots 5
nrootssel 1
excitations cisd
refs cas(0,0) end
end
end
* int 0 1
C 0 0 0 0 0 0
O 1 0 0 1.2 0 0
H 1 2 0 1.1 120 0
H 1 2 3 1.1 120 180
*
The details are explained in the ORCA manual
(http://www.thch.uni-bonn.de/tc/orca/). If you want to do it for larger
molecules you have to manually select an orbital window (~200-300 MOs will be
possible depending on your computer). Concerning the physical content of such
CISD calculations of excited states i personally share the views of Mike Zerner
- you basically overcorrelate the ground state relative to the excited states
and will make things worse; also size-consistency problems will show up in the
results. Third, the parameterization is done for CIS and including the doubles
would require a change since you know treat part of the dynamic correlation
explicitly. Finally, it will get much more computationally expensive rather quickly.
Hope that helps,
all the best,
Frank
====
Thank you again and best regards,
Marianna
--
-----------------------------------------------------------------
Marianna Fanti, PhD, Dip. di Chimica "G. Ciamician" University of
Bologna, via Selmi 2, I-40126 Bologna, Italy, Fax: +39-0512099456
Phone +39-0512099521, http://www.ciam.unibo.it/models/mari
e-mail: marianna.fanti]=[unibo.it
-----------------------------------------------------------------
All that you take with you is what you leave behind
-----------------------------------------------------------------
From owner-chemistry@ccl.net Tue Apr 3 08:43:02 2007
From: "Fredrik Blomgren fredrik.blomgren|cit.chalmers.se" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: IRC calculation using GAMESS
Message-Id: <-33955-070403042140-28184-IOI/R7i+6XsUv1C5c7RWSg^server.ccl.net>
X-Original-From: "Fredrik Blomgren" <fredrik.blomgren_._cit.chalmers.se>
Date: Tue, 3 Apr 2007 04:21:35 -0400
Sent to CCL by: "Fredrik Blomgren" [fredrik.blomgren:-:cit.chalmers.se]
Dear All
I'm trying to perform an IRC calculation with GAMESS and have two problems. First I should say that my transition state is as fas as I can tell correct, so that is most likely not the problem.
Problem 1):
If I set up my IRC calculation using a small number for NPOINT, the entire IRC is not found. When I try to restart it using the restart information provided by the program in the *.dat file, I get the message:
RADIUS IN CIRCLE OPTIMIZATION 0.0067834 DEVIATES SIGNIFICANTLY FROM CONSTRAIN CONDITION 0.0050000
IT IS POSSIBLE THAT THE NEXT IRC POINT IS CLOSE TO A MINIMUM
I find it to be extremely unlikely that the system is near a minimum at exactly the point which corresponds to my setting of NPOINT. Does anybody know the fix for this problem? I guess what I am asking is how does one resart an IRC calculation correctly in GAMESS?
Problem 2)
When I ran into problem 1, I increased NPOINT and let the calculation run longer. Then eventually the calculation stopped with the same message (but this time at a point smaller than my setting of NPOINT):
RADIUS IN CIRCLE OPTIMIZATION 0.0067834 DEVIATES SIGNIFICANTLY FROM CONSTRAIN CONDITION 0.0050000
IT IS POSSIBLE THAT THE NEXT IRC POINT IS CLOSE TO A MINIMUM
This time it may be true that the system is near a minimum, I dont know. When I use the MacMolPlt-program and look at the potential enenrgy surface for the IRC-calculation the system appears NOT to be near a minimum. The potential energy surface is not curved at all for the last points in the IRC-calculation which is in my mind what should happen near the minimum. However, I can be wrong about this. Does anybody know how I should continue to reach the true minimum? I don't think I can restart using the information provided by the program because then I will run into problem 1.
Thanks in advance
Fredrik Blomgren
From owner-chemistry@ccl.net Tue Apr 3 10:31:01 2007
From: "Roman D. Gorbunov gorbunov*theochem.uni-frankfurt.de" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL:G: Units of the transition dipole moments in Gaussian output.
Message-Id: <-33956-070403102516-7768-W4UIxeGd8vyG3oemz8pPTw#%#server.ccl.net>
X-Original-From: "Roman D. Gorbunov" <gorbunov(0)theochem.uni-frankfurt.de>
Date: Tue, 3 Apr 2007 10:25:12 -0400
Sent to CCL by: "Roman D. Gorbunov" [gorbunov . theochem.uni-frankfurt.de]
Dear All,
I need to calculate transition dipole moments of a molecules (with the Gaussian program). I almost succeed with that. I know that in the input file I have to put "IOP(7/33=1)" and in the out put files I will find lines like the following:
Dipole derivatives wrt mode 1: 6.63698D-04 3.58316D-02 2.60498D+00
Dipole derivatives wrt mode 2: -8.98377D-03 -1.05618D-02 1.02878D+00
This is exactly what I need. The only problem is that I do not know the units in which the dipole transition dipole moments are given. Does anybody know that? Or may be somebody know where I can read that about?
Thanks,
Roman.
From owner-chemistry@ccl.net Tue Apr 3 12:10:01 2007
From: "Per Jr. Greisen pgreisen- -gmail.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: PM3 electronic density etc
Message-Id: <-33957-070403103245-9278-WqZzB7pbKs/mARKt/9zl/A[A]server.ccl.net>
X-Original-From: "Per Jr. Greisen" <pgreisen,gmail.com>
Content-Type: multipart/alternative;
boundary="----=_Part_11569_17410168.1175610738303"
Date: Tue, 3 Apr 2007 16:32:18 +0200
MIME-Version: 1.0
Sent to CCL by: "Per Jr. Greisen" [pgreisen() gmail.com]
------=_Part_11569_17410168.1175610738303
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Hi all
I have made some qm simulation of different molecules using gamess and if I
use PM3 it is not possible for me to visualize orbitals, electronic density,
or electrostatic potential - if I on the other hand use DFT or RHF it is no
problem - it that because of PM3 or should I active some specific out put in
gamess?
Any help or advice appreciated. Thanks in advance.
best regards
Per
------=_Part_11569_17410168.1175610738303
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Hi all<br><br>I have made some qm simulation of different molecules
using gamess and if I use PM3 it is not possible for me to visualize
orbitals, electronic density, or electrostatic potential - if I on the
other hand use DFT or RHF it is no problem - it that because of PM3 or
should I active some specific out put in gamess?
<br><br>Any help or advice appreciated. Thanks in advance.<br clear="all"> best regards <br>Per<br>
------=_Part_11569_17410168.1175610738303--
From owner-chemistry@ccl.net Tue Apr 3 13:10:01 2007
From: "Sachin Tyagi sachintyagi1__gmail.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: Input file
Message-Id: <-33958-070403121742-16443-01b+x5BRaySQ7yp4JvqauA__server.ccl.net>
X-Original-From: "Sachin Tyagi" <sachintyagi1#%#gmail.com>
Date: Tue, 3 Apr 2007 12:17:38 -0400
Sent to CCL by: "Sachin Tyagi" [sachintyagi1 .. gmail.com]
Hi can anybody please tell me or show me example of, how to put two molecules in one input file. I want to find the transition state using QST2/QST3 keywords.
Thanks
Sachin
From owner-chemistry@ccl.net Tue Apr 3 14:41:01 2007
From: "Shobe, David David.Shobe===sud-chemie.com" <owner-chemistry+*+server.ccl.net>
To: CCL
Subject: CCL: Input file
Message-Id: <-33959-070403140444-5450-BbgGIWqRr2KLrAsDdmnSfQ+*+server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe|*|sud-chemie.com>
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Date: Tue, 3 Apr 2007 20:04:24 +0200
MIME-Version: 1.0
Sent to CCL by: "Shobe, David" [David.Shobe()sud-chemie.com]
Sachin,
With some front-ends you have to save each geometry (initial, TS, final) as a separate file, and then use a text editor to cut and paste everything together. Construct and save the initial geometry and then !important! modify the initial geometry to form the TS and then the product. If you build each geometry from scratch you're much more likely to make a mistake.
Regards,
--David Shobe
S�d-Chemie, Inc.
Attention to detial is essentail.
-----Original Message-----
> From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net]
Sent: Tuesday, April 03, 2007 12:18 PM
To: Shobe, David
Subject: CCL: Input file
Sent to CCL by: "Sachin Tyagi" [sachintyagi1 .. gmail.com]
Hi can anybody please tell me or show me example of, how to put two molecules in one input file. I want to find the transition state using QST2/QST3 keywords.
Thanks
Sachinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message.
Thank you.
From owner-chemistry@ccl.net Tue Apr 3 18:00:00 2007
From: "Cory Pye cpye-#-crux.smu.ca" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Input file
Message-Id: <-33960-070403174525-30290-fbHvn1kyfXel/BuO7rteQg++server.ccl.net>
X-Original-From: Cory Pye <cpye---crux.smu.ca>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Tue, 3 Apr 2007 18:45:14 -0300 (ADT)
MIME-Version: 1.0
Sent to CCL by: Cory Pye [cpye(~)crux.smu.ca]
Hello CCLers (esp Sachin Tyagi),
Here is an example of an input file for a QST3 calc. This was a particularly
nasty TS to find, as numerous calculations with an MP2/6-31g* geometry, MO
guess and Hessian guess failed. It is the fragmentation of a methyltriazenyl
anion into dinitrogen and methylamide ion.
-Cory
%rwf=/disc34/tmp/cpye/
%NoSave
%chk=HNNNMe_-_ZE_frag_LST
%mem=512Mb
#N mp2/6-31+g* FOpt=(CalcFC,QST3,Path=20) Freq
Reactant
-1 1
N1
N2 N1 N2N
N3 N2 N3N N1 N3NN
C1 N1 C1N N2 C1NN N3 C1NNN
H3 N3 H3N N2 H3NN N1 H3NNN
H1A C1 H1AC N1 H1ACN N2 H1ACNN
H1B C1 H1BC N1 H1BCN N2 H1BCNN
H1C C1 H1CC N1 H1CCN N2 H1CCNN
N2N=1.31101371
N3N=1.33796951
C1N=1.46397532
H3N=1.02857358
H1AC=1.10399525
H1BC=1.10398579
H1CC=1.09605862
N3NN=117.59023611
C1NN=113.7780536
H3NN=102.23467989
H1ACN=111.69183183
H1BCN=111.69453409
H1CCN=107.37189862
C1NNN=-0.00019353
H3NNN=179.98234974
H1ACNN=58.98790887
H1BCNN=-58.96527311
H1CCNN=-179.99289758
Product
-1 1
N1
N2 N1 N2N
N3 N2 N3N N1 N3NN
C1 N3 C1N N2 C1NN N1 C1NNN
H3 N3 H3N N2 H3NN N1 H3NNN
H1A C1 H1AC N3 H1ACN N2 H1ACNN
H1B C1 H1BC N3 H1BCN N2 H1BCNN
H1C C1 H1CC N3 H1CCN N2 H1CCNN
N2N=1.13207902
N3N=3.04265528
C1N=1.45150012
H3N=1.03197083
H1AC=1.12375843
H1BC=1.10417449
H1CC=1.12375896
N3NN=79.28215429
C1NN=97.34347942
H3NN=153.85360832
H1ACN=116.73763699
H1BCN=108.72680796
H1CCN=116.73752364
C1NNN=91.43934317
H3NNN=247.36411848
H1ACNN=107.25877488
H1BCNN=-10.80295899
H1CCNN=231.1350411
Guess TS
-1 1
N1
N2 N1 N2N
N3 N2 N3N N1 N3NN
C1 N1 C1N N2 C1NN N3 C1NNN
H3 N3 H3N N2 H3NN N1 H3NNN
H1A C1 H1AC N1 H1ACN N2 H1ACNN
H1B C1 H1BC N1 H1BCN N2 H1BCNN
H1C C1 H1CC N1 H1CCN N2 H1CCNN
N2N=1.21224981
N3N=1.38484928
C1N=2.40729226
H3N=1.04350867
H1AC=1.0915791
H1BC=1.10057133
H1CC=1.09297596
N3NN=119.20689995
C1NN=84.3980526
H3NN=105.78763147
H1ACN=89.3916906
H1BCN=147.70058149
H1CCN=85.98798999
C1NNN=-8.19672365
H3NNN=127.38226186
H1ACNN=124.76474511
H1BCNN=-2.41252662
H1CCNN=-124.60993488
On Tue, 3 Apr 2007, Shobe, David David.Shobe===sud-chemie.com wrote:
>
> Sent to CCL by: "Shobe, David" [David.Shobe()sud-chemie.com]
> Sachin,
>
> With some front-ends you have to save each geometry (initial, TS, final) as a separate file, and then use a text editor to cut and paste everything together. Construct and save the initial geometry and then !important! modify the initial geometry to form the TS and then the product. If you build each geometry from scratch you're much more likely to make a mistake.
>
> -----Original Message-----
> > From: owner-chemistry##ccl.net [mailto:owner-chemistry##ccl.net]
> Sent: Tuesday, April 03, 2007 12:18 PM
> To: Shobe, David
> Subject: CCL: Input file
>
>
> Sent to CCL by: "Sachin Tyagi" [sachintyagi1 .. gmail.com]
> Hi can anybody please tell me or show me example of, how to put two molecules in one input file. I want to find the transition state using QST2/QST3 keywords.
>
> Thanks
>
************* ! Dr. Cory C. Pye
***************** ! Associate Professor
*** ** ** ** ! Theoretical and Computational Chemistry
** * **** ! Department of Chemistry, Saint Mary's University
** * * ! 923 Robie Street, Halifax, NS B3H 3C3
** * * ! cpye(0)crux.stmarys.ca http://apwww.stmarys.ca/~cpye
*** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104
***************** !
************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans)
From owner-chemistry@ccl.net Tue Apr 3 21:45:01 2007
From: "Dan C Fara dfara%x%salud.unm.edu" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: melting point
Message-Id: <-33961-070403114646-8695-wyHnzV6jNE4KS/7no6CETA=server.ccl.net>
X-Original-From: "Dan C Fara" <dfara[]salud.unm.edu>
Date: Tue, 3 Apr 2007 11:46:42 -0400
Sent to CCL by: "Dan C Fara" [dfara!A!salud.unm.edu]
Dear All:
Is there any free software that can be used for estimating the melting point values of organic compounds?
Thanks.
Dan Fara
Univ. of New Mexico, Division of Biocomputing
From owner-chemistry@ccl.net Tue Apr 3 23:23:01 2007
From: "Soren Eustis soren_+_jhu.edu" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: melting point
Message-Id: <-33962-070403232123-16884-Vv8/lDI8lg6si7vU9T00wg*_*server.ccl.net>
X-Original-From: "Soren Eustis" <soren*_*jhu.edu>
Content-Language: en-us
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset="us-ascii"
Date: Tue, 3 Apr 2007 23:20:17 -0400
MIME-Version: 1.0
Sent to CCL by: "Soren Eustis" [soren##jhu.edu]
The EPA EPIWin package can do this. Go to epa.gov and search for epiwin.
You ought to be able to find it.
Soren Eustis
-----Original Message-----
> From: owner-chemistry~!~ccl.net [mailto:owner-chemistry~!~ccl.net]
Sent: Tuesday, April 03, 2007 11:47 AM
To: Eustis, Soren
Subject: CCL: melting point
Sent to CCL by: "Dan C Fara" [dfara!A!salud.unm.edu]
Dear All:
Is there any free software that can be used for estimating the melting point
values of organic compounds?
Thanks.
Dan Fara
Univ. of New Mexico, Division of Biocomputinghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt