From owner-chemistry@ccl.net Mon May 25 04:36:01 2009
From: "Tristan Youngs t.youngs---qub.ac.uk" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Aten v1.2 released.
Message-Id: <-39366-090525042932-4821-bw1ZOBd3vWPkFlEC2pXSCg||server.ccl.net>
X-Original-From: "Tristan Youngs" <t.youngs a qub.ac.uk>
Date: Mon, 25 May 2009 04:29:27 -0400
Sent to CCL by: "Tristan Youngs" [t.youngs_-_qub.ac.uk]
After many months of toil (and doing other things) the new version of Aten is ready for use, and hopefully ready to tackle more configuration building, editing, and visualisation needs.
Version 1.2 brings about a completely re-written scripting language, since the old one was more than a little clunky. The new, C-style syntax is far more powerful, and far more useful (as it turns out) on a day-to-day basis! This enhancement comes at the cost of filter/script incompatibility with earlier versions, but conversion is mostly a trivial matter of adding parentheses and semicolons to function calls.
Visit http://www.projectaten.net and see if Aten can be useful for you - downloads for Linux, Mac, and Windows are all available. Bugfixes, comments, and suggestions welcome as always.
Cheers,
Tris.
tris%a%projectaten.net
t.youngs%a%qub.ac.uk
From owner-chemistry@ccl.net Mon May 25 05:20:01 2009
From: "Saurabh Agrawal Saurabh.Agrawal!A!ucdconnect.ie" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL:G: Experimental and theratical UV calculation
Message-Id: <-39367-090523145839-18122-DPZiv7JIofsr63Ied2eyNQ||server.ccl.net>
X-Original-From: Saurabh Agrawal <Saurabh.Agrawal,+,ucdconnect.ie>
Content-language: en
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boundary="Boundary_(ID_b0Z36MatgPJrL0f9DQrDQQ)"
Date: Sat, 23 May 2009 18:57:52 +0100
MIME-version: 1.0
Sent to CCL by: Saurabh Agrawal [Saurabh.Agrawal---ucdconnect.ie]
This is a multi-part message in MIME format.
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Hello,
I have calculated UV=A0absorption spectrum for some molecules using G=
aussian. With the following basis set and cards.
#p B3LYP/6-31g** TD(Singlet,NSTATES=3D15) guess=3Dread geom=3Dcheck
The results I got are considerably different from experimental result=
s.=20
1) Can we compare the theoretical results with experimental results? =
I appreciate if some one could send link for some basic notes on it.
Sincere regards,
Saurabh
Saurabh=A0Agrawal,
PhD Student,
Department of Chemical and Bioprocess=A0Engineering,
UCD, Belfield,
Dublin-4, Ireland
--Boundary_(ID_b0Z36MatgPJrL0f9DQrDQQ)
Content-type: text/html; charset=us-ascii
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Content-disposition: inline
Hello,<br><br>I have calculated UV absorption spectrum for some molecules using Gaussian. With the following basis set and cards.<br><br>#p B3LYP/6-31g** TD(Singlet,NSTATES=15) guess=read geom=check<br><br>The results I got are considerably different from experimental results. <br><br>1) Can we compare the theoretical results with experimental results? I appreciate if some one could send link for some basic notes on it.<br><br>Sincere regards,<br><br>Saurabh<br><br><br><br>Saurabh Agrawal,<br>PhD Student,<br>Department of Chemical and Bioprocess Engineering,<br>UCD, Belfield,<br>Dublin-4, Ireland<br>
--Boundary_(ID_b0Z36MatgPJrL0f9DQrDQQ)--
From owner-chemistry@ccl.net Mon May 25 06:40:01 2009
From: "Ismael Ortiz Verano ieortizv*bt.unal.edu.co" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL:G: Experimental and theratical UV calculation
Message-Id: <-39368-090525063605-6969-iYM6M3jSg3Kpik6ydboLbQ+/-server.ccl.net>
X-Original-From: Ismael Ortiz Verano <ieortizv]*[bt.unal.edu.co>
Content-Type: multipart/alternative; boundary=0003255749ca92ba84046aba2ca8
Date: Mon, 25 May 2009 05:35:31 -0500
MIME-Version: 1.0
Sent to CCL by: Ismael Ortiz Verano [ieortizv-x-bt.unal.edu.co]
--0003255749ca92ba84046aba2ca8
Content-Type: text/plain; charset=ISO-8859-1
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Saurabh
Perhaps 15 states are not sufficient, and in order to get accord with the
experiment, you can calculate more states (try 40 or 50).
I think that when you compare your theoretical results, you obtain only
wavelenghts of low energy (red).
If you are looking for a better accord, you can carry out a calculation tha=
t
includes solvent's effect.
--=20
Ismael Ortiz
Grupo de Qu=EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (57)(1) 3165000 ext 10608
2009/5/23 Saurabh Agrawal Saurabh.Agrawal!A!ucdconnect.ie <
owner-chemistry=ccl.net>
> Hello,
>
> I have calculated UV absorption spectrum for some molecules using Gaussia=
n.
> With the following basis set and cards.
>
> #p B3LYP/6-31g** TD(Singlet,NSTATES=3D15) guess=3Dread geom=3Dcheck
>
> The results I got are considerably different from experimental results.
>
> 1) Can we compare the theoretical results with experimental results? I
> appreciate if some one could send link for some basic notes on it.
>
> Sincere regards,
>
> Saurabh
>
>
>
> Saurabh Agrawal,
> PhD Student,
> Department of Chemical and Bioprocess Engineering,
> UCD, Belfield,
> Dublin-4, Ireland
>
--=20
Ismael Ortiz Verano
Grupo de Qu=EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (57)(1) 3165000 ext 10608
--0003255749ca92ba84046aba2ca8
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Saurabh<br><br>Perhaps 15 states are not sufficient, and in order to get ac=
cord with the experiment, you can calculate more states (try 40 or 50).<br>=
<br>I think that when you compare your theoretical results, you obtain only=
wavelenghts of low energy (red). <br>
<br>If you are looking for a better accord, you can carry out a calculation=
that includes solvent's effect.<br><br>-- <br>Ismael Ortiz<br>Grupo de=
Qu=EDmica Te=F3rica<br>Universidad Nacional de Colombia<br>Tel: (57)(1) 31=
65000 ext 10608<br>
<br><br><div class=3D"gmail_quote">2009/5/23 Saurabh Agrawal Saurabh.Agrawa=
l!A!<a href=3D"http://ucdconnect.ie">ucdconnect.ie</a> <span dir=3D"ltr">&l=
t;<a href=3D"mailto:owner-chemistry=ccl.net">owner-chemistry=ccl.net</a>>=
;</span><br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hello,<br><br>I h=
ave calculated UV=A0absorption spectrum for some molecules using Gaussian. =
With the following basis set and cards.<br>
<br>#p B3LYP/6-31g** TD(Singlet,NSTATES=3D15) guess=3Dread geom=3Dcheck<br>=
<br>The results I got are considerably different from experimental results.=
<br><br>1) Can we compare the theoretical results with experimental result=
s? I appreciate if some one could send link for some basic notes on it.<br>
<br>Sincere regards,<br><br>Saurabh<br><br><br><br>Saurabh=A0Agrawal,<br>Ph=
D Student,<br>Department of Chemical and Bioprocess=A0Engineering,<br>UCD, =
Belfield,<br>Dublin-4, Ireland<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Ismael Ortiz Verano<br>=
Grupo de Qu=EDmica Te=F3rica<br>Universidad Nacional de Colombia<br>Tel: (5=
7)(1) 3165000 ext 10608<br>
--0003255749ca92ba84046aba2ca8--
From owner-chemistry@ccl.net Mon May 25 08:43:00 2009
From: "Mahmoud A. A. Ibrahim m.ibrahim1982],[yahoo.com" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL:G: Experimental and theratical UV calculation
Message-Id: <-39369-090525083030-27481-RXas2LdUfOhuJ7NBQRbQog%server.ccl.net>
X-Original-From: "Mahmoud A. A. Ibrahim" <m.ibrahim1982|yahoo.com>
Content-Type: multipart/alternative; boundary="0-1721251397-1243251014=:82131"
Date: Mon, 25 May 2009 04:30:14 -0700 (PDT)
MIME-Version: 1.0
Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982|a|yahoo.com]
--0-1721251397-1243251014=:82131
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable
Dear Saurabh=20
Sure we can, we can compare theoretical calculations with the experimental =
one.
But you should be aware of some points, firstly, your structure should be t=
he optimized one (I don't mean here after optimization, I mean your structu=
re is the structure of the experimental one under solvation effect).
About, the number of states, it is depending on you experimental one, for e=
xample your experimental lamda max is around 280nm (for example) and your r=
un your TD calculation based on 10 states and found the your excitation sta=
tes didn't reached the desired one (i.e. 280nm) and stops at 300nm, so you =
should Add more states. So, there is no optimum number of states. You start=
with small number and then add more states until reach your desired wavele=
ngth.
Sure, solvation has a big big effect on your TD calculations and on all cal=
culations in general. And here I would like to send a small experience in s=
tudying solvation effect, DON'T Trust always in solvation modeling, Some ti=
mes you have to add explicit water molecules.
Through out the last of weeks I was doing theoretical UV Data for some comp=
lexes, so if you like me to have a look on your UV spectra (theoretical and=
expremental one), send it.
But, there is one keyword I couldn't understand its effect, it is called Eq=
Solv. It says makes equilibrium solvation on your system using PCM model. B=
ut, it doesn't add solvation model and you need to add solvation model keyw=
ord in addition to Eqsolv.
I would like to push you forward and say you can get the same exactly UV sp=
ectra theoretical as the experimental one, but the problem is to mimic your=
system well.
Sincerely;
M. Ibrahim
Mahmoud A. A. Ibrahim
Current Address
School of Chemistry, University of Manchester,=20
Oxford Road, Manchester, M13 9PL, United Kingdom.
Mahmoud.Ibrahim-2:-:postgrad.manchester.ac.uk=20
=20
Home Address =20
Chemistry Department, Faculty of Science,=20
Minia University,=20
Minia 61519,Egypt.=20
M.Ibrahim1982:-:yahoo.com=20
Mobile Phone No.: +20102554083 =20
Land Phone No.: +20226635916=20
Fax No.: +20862342601
--- On Mon, 5/25/09, Ismael Ortiz Verano ieortizv*bt.unal.edu.co <owner-che=
mistry:-:ccl.net> wrote:
> From: Ismael Ortiz Verano ieortizv*bt.unal.edu.co <owner-chemistry:-:ccl.net>
Subject: CCL:G: Experimental and theratical UV calculation
To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982:-:yahoo.com>
Date: Monday, May 25, 2009, 11:35 AM
Saurabh
Perhaps 15 states are not sufficient, and in order to get accord with the e=
xperiment, you can calculate more states (try 40 or 50).
I think that when you compare your theoretical results, you obtain only wav=
elenghts of low energy (red).=20
=0A=0A
If you are looking for a better accord, you can carry out a calculation tha=
t includes solvent's effect.
--=20
Ismael Ortiz
Grupo de Qu=EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (57)(1) 3165000 ext 10608
=0A=0A
2009/5/23 Saurabh Agrawal Saurabh.Agrawal!A!ucdconnect.ie <owner-chemistry*=
o*ccl.net>
=0A=0AHello,
I have calculated UV=A0absorption spectrum for some molecules using Gaussia=
n. With the following basis set and cards.
=0A=0A
#p B3LYP/6-31g** TD(Singlet,NSTATES=3D15) guess=3Dread geom=3Dcheck
The results I got are considerably different from experimental results.=20
1) Can we compare the theoretical results with experimental results? I appr=
eciate if some one could send link for some basic notes on it.
=0A=0A
Sincere regards,
Saurabh
Saurabh=A0Agrawal,
PhD Student,
Department of Chemical and Bioprocess=A0Engineering,
UCD, Belfield,
Dublin-4, Ireland
=0A
--=20
Ismael Ortiz Verano
Grupo de Qu=EDmica Te=F3rica
Universidad Nacional de Colombia
Tel: (57)(1) 3165000 ext 10608
=0A=0A=0A=0A
--0-1721251397-1243251014=:82131
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable
<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;">Dear Saurabh <br>Sure we can, we can compare =
theoretical calculations with the experimental one.<br>But you should be aw=
are of some points, firstly, your structure should be the optimized one (I =
don't mean here after optimization, I mean your structure is the structure =
of the <span>experimental</span> one under solvation effect).<br>About, the=
number of states, it is depending on you experimental one, for example you=
r experimental lamda max is around 280nm (for example) and your run your TD=
calculation based on 10 states and found the your excitation states didn't=
reached the desired one (i.e. 280nm) and stops at 300nm, so you should Add=
more states. So, there is no optimum number of states. You start with smal=
l number and then add more states until reach your desired wavelength.<br>S=
ure, solvation has a big big effect on your TD calculations and on all
calculations in general. And here I would like to send a small experience =
in studying solvation effect, DON'T Trust always in solvation modeling, Som=
e times you have to add explicit water molecules.<br>Through out the last o=
f weeks I was doing theoretical UV Data for some complexes, so if you like =
me to have a look on your UV spectra (theoretical and expremental one), sen=
d it.<br>But, there is one keyword I couldn't understand its effect, it is =
called EqSolv. It says makes equilibrium solvation on your system using PCM=
model. But, it doesn't add solvation model and you need to add solvation m=
odel keyword in addition to Eqsolv.<br>I would like to push you forward and=
say you can get the same exactly UV spectra theoretical as the experimenta=
l one, but the problem is to mimic your system well.<br>Sincerely;<br>M. Ib=
rahim<br><br><div style=3D"text-align: center;"><span style=3D"font-weight:=
bold; font-style: italic;">Mahmoud A. A. Ibrahim</span><br></div><span
style=3D"font-weight: bold;"><br></span><div style=3D"text-align: center;"=
><span style=3D"font-weight: bold;">Current Address</span><br></div><div st=
yle=3D"margin-left: 40px; text-align: center;">School of Chemistry, Univers=
ity of Manchester, <br>Oxford Road, Manchester, M13 9PL, United Kingdom.<br=
>Mahmoud.Ibrahim-2:-:postgrad.manchester.ac.uk <br></div> <br><div style=3D"t=
ext-align: center;"><span style=3D"font-weight: bold;"> Home =
Address </span><br></div><div style=3D"margin-left: 40px;=
"><div style=3D"text-align: center;"> Chemistry Department, Faculty of S=
cience, <br> <span>Minia</span> University, <br> M=
inia 61519,Egypt. <br> M.Ibrahim1982:-:yahoo.com <br> Mobile Pho=
ne No.: +20102554083 <br></div><div style=3D"text-align: center;"> L=
and Phone No.: +20226635916 <br> Fax No.: +20862342601</div></div=
><br><br>--- On <b>Mon, 5/25/09, Ismael Ortiz Verano ieortizv*bt.unal.edu.c=
o
<i><owner-chemistry:-:ccl.net></i></b> wrote:<br><blockquote style=3D"=
border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5p=
x;"><br>From: Ismael Ortiz Verano ieortizv*bt.unal.edu.co <owner-chemist=
ry:-:ccl.net><br>Subject: CCL:G: Experimental and theratical UV calculatio=
n<br>To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982:-:yahoo.com><=
br>Date: Monday, May 25, 2009, 11:35 AM<br><br><div id=3D"yiv96937592">Saur=
abh<br><br>Perhaps 15 states are not sufficient, and in order to get accord=
with the experiment, you can calculate more states (try 40 or 50).<br><br>=
I think that when you compare your theoretical results, you obtain only wav=
elenghts of low energy (red). <br>=0A=0A<br>If you are looking for a better=
accord, you can carry out a calculation that includes solvent's effect.<br=
><br>-- <br>Ismael Ortiz<br>Grupo de Qu=EDmica Te=F3rica<br>Universidad Nac=
ional de Colombia<br>Tel: (57)(1) 3165000 ext 10608<br>=0A=0A<br><br><div c=
lass=3D"gmail_quote">2009/5/23 Saurabh Agrawal Saurabh.Agrawal!A!<a rel=3D"=
nofollow" target=3D"_blank" href=3D"http://ucdconnect.ie">ucdconnect.ie</a>=
<span dir=3D"ltr"><<a rel=3D"nofollow" ymailto=3D"mailto:owner-chemistr=
y*o*ccl.net" target=3D"_blank" href=3D"/mc/compose?to=3Downer-chemistry*o*c=
cl.net">owner-chemistry*o*ccl.net</a>></span><br>=0A=0A<blockquote class=
=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, 204, 204); margin=
: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hello,<br><br>I have calculated UV=
absorption spectrum for some molecules using Gaussian. With the follo=
wing basis set and cards.<br>=0A=0A<br>#p B3LYP/6-31g** TD(Singlet,NSTATES=
=3D15) guess=3Dread geom=3Dcheck<br><br>The results I got are considerably =
different from experimental results. <br><br>1) Can we compare the theoreti=
cal results with experimental results? I appreciate if some one could send =
link for some basic notes on it.<br>=0A=0A<br>Sincere regards,<br><br>Saura=
bh<br><br><br><br>Saurabh Agrawal,<br>PhD Student,<br>Department of Ch=
emical and Bioprocess Engineering,<br>UCD, Belfield,<br>Dublin-4, Irel=
and<br>=0A</blockquote></div><br><br clear=3D"all"><br>-- <br>Ismael Ortiz =
Verano<br>Grupo de Qu=EDmica Te=F3rica<br>Universidad Nacional de Colombia<=
br>Tel: (57)(1) 3165000 ext 10608<br>=0A</div></blockquote></td></tr></tabl=
e><br>=0A=0A=0A=0A
--0-1721251397-1243251014=:82131--
From owner-chemistry@ccl.net Mon May 25 11:16:01 2009
From: "David Gallagher gallagher.da::gmail.com" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL:G: Experimental and theratical UV calculation
Message-Id: <-39370-090525111248-18831-AM0UO36eQGtpRkR9CD3Aog+/-server.ccl.net>
X-Original-From: David Gallagher <gallagher.da(~)gmail.com>
Content-Type: multipart/alternative;
boundary="=====================_11280046==.ALT"
Date: Mon, 25 May 2009 08:12:19 -0700
Mime-Version: 1.0
Sent to CCL by: David Gallagher [gallagher.da-x-gmail.com]
--=====================_11280046==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed
Hi Saurabh,
There are various issues that can explain possible discrepancies
between experimental and theoretical UV spectra, including geometry,
solvation and vibrational fine structure, etc. The key issues are
discussed and illustrated in a slide presentation posted at
<http://cacheresearch.com/presentations.html>http://cacheresearch.com/presentations.html
(top of page).
I hope this helps.
Regards,
David Gallagher
CACheResearch.com
At 10:57 AM 5/23/2009, Saurabh Agrawal Saurabh.Agrawal!A!ucdconnect.ie wrote:
>Hello,
>
>I have calculated UV absorption spectrum for some molecules using
>Gaussian. With the following basis set and cards.
>
>#p B3LYP/6-31g** TD(Singlet,NSTATES=15) guess=read geom=check
>
>The results I got are considerably different from experimental results.
>
>1) Can we compare the theoretical results with experimental results?
>I appreciate if some one could send link for some basic notes on it.
>
>Sincere regards,
>
>Saurabh
>
>
>
>Saurabh Agrawal,
>PhD Student,
>Department of Chemical and Bioprocess Engineering,
>UCD, Belfield,
>Dublin-4, Ireland
--=====================_11280046==.ALT
Content-Type: text/html; charset="us-ascii"
<html>
<body>
Hi Saurabh,<br><br>
There are various issues that can explain possible discrepancies between
experimental and theoretical UV spectra, including geometry, solvation
and vibrational fine structure, etc. The key issues are discussed
and illustrated in a slide presentation posted at
<a href="http://cacheresearch.com/presentations.html">
http://cacheresearch.com/presentations.html</a> (top of page).<br><br>
I hope this helps.<br>
Regards,<br>
David Gallagher<br>
CACheResearch.com<br><br>
<br>
At 10:57 AM 5/23/2009, Saurabh Agrawal Saurabh.Agrawal!A!ucdconnect.ie
wrote:<br>
<blockquote type=cite class=cite cite="">Hello,<br><br>
I have calculated UV absorption spectrum for some molecules using
Gaussian. With the following basis set and cards.<br><br>
#p B3LYP/6-31g** TD(Singlet,NSTATES=15) guess=read geom=check<br><br>
The results I got are considerably different from experimental results.
<br><br>
1) Can we compare the theoretical results with experimental results? I
appreciate if some one could send link for some basic notes on
it.<br><br>
Sincere regards,<br><br>
Saurabh<br><br>
<br><br>
Saurabh Agrawal,<br>
PhD Student,<br>
Department of Chemical and Bioprocess Engineering,<br>
UCD, Belfield,<br>
Dublin-4, Ireland</blockquote></body>
</html>
--=====================_11280046==.ALT--
From owner-chemistry@ccl.net Mon May 25 12:19:01 2009
From: "John McKelvey jmmckel[*]gmail.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: Experimental and theratical UV calculation
Message-Id: <-39371-090525103646-17672-V2krR9zCct+W7wrobbVq0A!=!server.ccl.net>
X-Original-From: John McKelvey <jmmckel()gmail.com>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 25 May 2009 10:36:32 -0400
MIME-Version: 1.0
Sent to CCL by: John McKelvey [jmmckel(!)gmail.com]
Hello..
It is not surpricing that Mike Zerner adjusted parameters for atoms to
get good results for his semiempirical INDO/S method; however I heard
him say 'There's nothing so semiempirical as an ab initio
calculation." I've worked with either or both semiempirical or ab
initio type methods for the last 45 years and am in complete agreement
with Mike. I have yet to see any "black box" approach that does not
have to be calibrated. To wit: "One swallow does not make a spring"
... one accurate calculation does not mean the next one will be.
I'm not being cynical but realistic BUT though retired from industry
I'm still looking for better and better "black boxes," and means to
improve approaches to use them and their results.
The never ending challenge for me is "absolute accuracy" versus
"predictability and reliability." An example out of Andy
Streitweser's group at Berkley.. A student or post-doc calculated the
deprotonation energies of a series of cyclic hydrocarbons using the
then new CNDO method. He then compared those delta E's with
experimentally determined experimental values and got an excellent
linear correlation! HOWEVER the slope of the line had the wrong
algebraic sign!!! Accurate? NO! Predictable? YES! Useful? YES!
Please be patient..
John McKelvey
On 5/25/09, Mahmoud A. A. Ibrahim m.ibrahim1982],[yahoo.com
<owner-chemistry_._ccl.net> wrote:
> Dear Saurabh
> Sure we can, we can compare theoretical calculations with the experimenta=
l
> one.
> But you should be aware of some points, firstly, your structure should be
> the optimized one (I don't mean here after optimization, I mean your
> structure is the structure of the experimental one under solvation effect=
).
> About, the number of states, it is depending on you experimental one, for
> example your experimental lamda max is around 280nm (for example) and you=
r
> run your TD calculation based on 10 states and found the your excitation
> states didn't reached the desired one (i.e. 280nm) and stops at 300nm, so
> you should Add more states. So, there is no optimum number of states. You
> start with small number and then add more states until reach your desired
> wavelength.
> Sure, solvation has a big big effect on your TD calculations and on all
> calculations in general. And here I would like to send a small experience=
in
> studying solvation effect, DON'T Trust always in solvation modeling, Some
> times you have to add explicit water molecules.
> Through out the last of weeks I was doing theoretical UV Data for some
> complexes, so if you like me to have a look on your UV spectra (theoretic=
al
> and expremental one), send it.
> But, there is one keyword I couldn't understand its effect, it is called
> EqSolv. It says makes equilibrium solvation on your system using PCM mode=
l.
> But, it doesn't add solvation model and you need to add solvation model
> keyword in addition to Eqsolv.
> I would like to push you forward and say you can get the same exactly UV
> spectra theoretical as the experimental one, but the problem is to mimic
> your system well.
> Sincerely;
> M. Ibrahim
>
> Mahmoud A. A. Ibrahim
>
> Current Address
> School of Chemistry, University of Manchester,
> Oxford Road, Manchester, M13 9PL, United Kingdom.
> Mahmoud.Ibrahim-2^postgrad.manchester.ac.uk
>
> Home Address
> Chemistry Department, Faculty of Science,
> Minia University,
> Minia 61519,Egypt.
> M.Ibrahim1982^yahoo.com
> Mobile Phone No.: +20102554083
> Land Phone No.: +20226635916
> Fax No.: +20862342601
>
> --- On Mon, 5/25/09, Ismael Ortiz Verano ieortizv*bt.unal.edu.co
> <owner-chemistry^ccl.net> wrote:
>
>> From: Ismael Ortiz Verano ieortizv*bt.unal.edu.co
>> <owner-chemistry^ccl.net>
> Subject: CCL:G: Experimental and theratical UV calculation
> To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982^yahoo.com>
> Date: Monday, May 25, 2009, 11:35 AM
>
> Saurabh
>
> Perhaps 15 states are not sufficient, and in order to get accord with the
> experiment, you can calculate more states (try 40 or 50).
>
> I think that when you compare your theoretical results, you obtain only
> wavelenghts of low energy (red).
>
>
>
> If you are looking for a better accord, you can carry out a calculation t=
hat
> includes solvent's effect.
>
> --
> Ismael Ortiz
> Grupo de Qu=EDmica Te=F3rica
> Universidad Nacional de Colombia
> Tel: (57)(1) 3165000 ext 10608
>
>
>
>
> 2009/5/23 Saurabh Agrawal Saurabh.Agrawal!A!ucdconnect.ie
> <owner-chemistry*o*ccl.net>
>
>
> Hello,
>
> I have calculated UV=A0absorption spectrum for some molecules using Gauss=
ian.
> With the following basis set and cards.
>
>
>
> #p B3LYP/6-31g** TD(Singlet,NSTATES=3D15) guess=3Dread geom=3Dcheck
>
> The results I got are considerably different from experimental results.
>
> 1) Can we compare the theoretical results with experimental results? I
> appreciate if some one could send link for some basic notes on it.
>
>
>
> Sincere regards,
>
> Saurabh
>
>
>
> Saurabh=A0Agrawal,
> PhD Student,
> Department of Chemical and Bioprocess=A0Engineering,
> UCD, Belfield,
> Dublin-4, Ireland
>
>
>
>
> --
> Ismael Ortiz Verano
> Grupo de Qu=EDmica Te=F3rica
> Universidad Nacional de Colombia
> Tel: (57)(1) 3165000 ext 10608
>
>
>
>
>
From owner-chemistry@ccl.net Mon May 25 13:27:01 2009
From: "Jan Moens molukken*_*hotmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: NON-equilibrium PCM calculation in Gaussian
Message-Id: <-39372-090525094219-26121-l/GvznfEo2jKzjpeqd4OjQ,+,server.ccl.net>
X-Original-From: "Jan Moens" <molukken{}hotmail.com>
Date: Mon, 25 May 2009 09:42:15 -0400
Sent to CCL by: "Jan Moens" [molukken^hotmail.com]
Dear all,
I am interested in nonequilibrium PCM calculations for vertical ionization potentials. In the g03 manual, it is indicated that non equilibrium solvation can be performed using the NonEq=type PCM keyword. But this keyword is not described elsewhere in the manual. Does anyone know how to use this keyword in a correct way?
Thanks in advance
Jan Moens
PhD student
Vrije Universiteit Brussel
From owner-chemistry@ccl.net Mon May 25 14:02:01 2009
From: "Duy Le ttduyle a gmail.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: need help in gaussian ts search
Message-Id: <-39373-090525131222-13442-YPhohhTFJNORjHPuMVSccA^-^server.ccl.net>
X-Original-From: Duy Le <ttduyle()gmail.com>
Content-Type: multipart/alternative; boundary=0016e645ba42bbeac5046abfb521
Date: Mon, 25 May 2009 13:11:47 -0400
MIME-Version: 1.0
Sent to CCL by: Duy Le [ttduyle###gmail.com]
--0016e645ba42bbeac5046abfb521
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
Not sure what do you mean by "not the transition state i want to find".
However, the document in http://cacheresearch.com/presentations.html may
help.
Best wishes
D.
On Fri, May 22, 2009 at 9:26 AM, tran van tan tvtan|-|staff.dthu.edu.vn <
owner-chemistry:-:ccl.net> wrote:
>
> Sent to CCL by: "tran van tan" [tvtan[a]staff.dthu.edu.vn]
> Hello everybody!
> I want to find a transition state in gaussian with this input
> # opt=(calcfc,tight,gdiis,ts) freq ub3lyp/6-311+g(d,p) nosymm
>
> ts
>
> 0 2
> C
> C 1 B1
> H 2 B2 1 A1
> C 1 B3 2 A2 3
> D1
> N 4 B4 1 A3 2
> D2
> H 4 B5 1 A4 2
> D3
>
> B1 1.19117810
> B2 1.05686011
> B3 1.42940095
> B4 1.24698289
> B5 1.08948293
> A1 179.42682237
> A2 178.40506719
> A3 123.91641107
> A4 49.00000000
> D1 180.00000000
> D2 180.00000000
> D3 0.00000000
>
> but the the result is not the transition state i want to find
>
> I also use qst2 method in gaussian but the result is not different
>
> # opt=qst2 b3lyp/6-311+g(d,p) freq
>
> re
>
> 0 2
> C
> C 1 B1
> H 2 B2 1 A1
> C 1 B3 2 A2 3
> D1
> N 4 B4 1 A3 2
> D2
> H 4 B5 1 A4 2
> D3
>
> B1 1.19117810
> B2 1.05686011
> B3 1.42940095
> B4 1.24698289
> B5 1.08948293
> A1 179.42682237
> A2 178.40506719
> A3 123.91641107
> A4 117.46164804
> D1 180.00000000
> D2 180.00000000
> D3 0.00000000
>
> Can you help me to find out my true transition state
> best regard>
>
>
--
Men don't need hands to do things!
--0016e645ba42bbeac5046abfb521
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Not sure what do you mean by "not the transition state i want to find&=
quot;. However, the document in <a href=3D"http://cacheresearch.com/present=
ations.html">http://cacheresearch.com/presentations.html</a> may help.<br>
Best wishes<br>D.<br><br><div class=3D"gmail_quote">On Fri, May 22, 2009 at=
9:26 AM, tran van tan tvtan|-|<a href=3D"http://staff.dthu.edu.vn">staff.d=
thu.edu.vn</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry:-:ccl.=
net">owner-chemistry:-:ccl.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: "tran van =A0tan" [tvtan[a]<a href=3D"http://staf=
f.dthu.edu.vn" target=3D"_blank">staff.dthu.edu.vn</a>]<br>
Hello everybody!<br>
I want to find a transition state in gaussian with this input<br>
# opt=3D(calcfc,tight,gdiis,ts) freq ub3lyp/6-311+g(d,p) nosymm<br>
<br>
ts<br>
<br>
0 2<br>
=A0C<br>
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B1<br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0B2 =A0=
=A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A1<br>
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B3 =A0=
=A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A2 =A0 =A03 =A0 =A0 =A0 =A0 =A0 =A0 =A0D1<=
br>
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0B4 =A0=
=A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A3 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0D2<=
br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0B5 =A0=
=A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A4 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0D3<=
br>
<br>
=A0 B1 =A0 =A0 =A0 =A0 =A0 =A0 1.19117810<br>
=A0 B2 =A0 =A0 =A0 =A0 =A0 =A0 1.05686011<br>
=A0 B3 =A0 =A0 =A0 =A0 =A0 =A0 1.42940095<br>
=A0 B4 =A0 =A0 =A0 =A0 =A0 =A0 1.24698289<br>
=A0 B5 =A0 =A0 =A0 =A0 =A0 =A0 1.08948293<br>
=A0 A1 =A0 =A0 =A0 =A0 =A0 179.42682237<br>
=A0 A2 =A0 =A0 =A0 =A0 =A0 178.40506719<br>
=A0 A3 =A0 =A0 =A0 =A0 =A0 123.91641107<br>
=A0 A4 =A0 =A0 =A0 =A0 =A0 =A049.00000000<br>
=A0 D1 =A0 =A0 =A0 =A0 =A0 180.00000000<br>
=A0 D2 =A0 =A0 =A0 =A0 =A0 180.00000000<br>
=A0 D3 =A0 =A0 =A0 =A0 =A0 =A0 0.00000000<br>
<br>
but the the result is not the transition state i want to find<br>
<br>
I also use qst2 method in gaussian but the result is not different<br>
<br>
# opt=3Dqst2 b3lyp/6-311+g(d,p) freq<br>
<br>
re<br>
<br>
0 2<br>
=A0C<br>
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B1<br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0B2 =A0=
=A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A1<br>
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0B3 =A0=
=A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0A2 =A0 =A03 =A0 =A0 =A0 =A0 =A0 =A0 =A0D1<=
br>
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0B4 =A0=
=A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A3 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0D2<=
br>
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A04 =A0 =A0 =A0 =A0 =A0 =A0 =A0B5 =A0=
=A01 =A0 =A0 =A0 =A0 =A0 =A0 =A0A4 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0D3<=
br>
<br>
=A0 B1 =A0 =A0 =A0 =A0 =A0 =A0 1.19117810<br>
=A0 B2 =A0 =A0 =A0 =A0 =A0 =A0 1.05686011<br>
=A0 B3 =A0 =A0 =A0 =A0 =A0 =A0 1.42940095<br>
=A0 B4 =A0 =A0 =A0 =A0 =A0 =A0 1.24698289<br>
=A0 B5 =A0 =A0 =A0 =A0 =A0 =A0 1.08948293<br>
=A0 A1 =A0 =A0 =A0 =A0 =A0 179.42682237<br>
=A0 A2 =A0 =A0 =A0 =A0 =A0 178.40506719<br>
=A0 A3 =A0 =A0 =A0 =A0 =A0 123.91641107<br>
=A0 A4 =A0 =A0 =A0 =A0 =A0 117.46164804<br>
=A0 D1 =A0 =A0 =A0 =A0 =A0 180.00000000<br>
=A0 D2 =A0 =A0 =A0 =A0 =A0 180.00000000<br>
=A0 D3 =A0 =A0 =A0 =A0 =A0 =A0 0.00000000<br>
<br>
Can you help me to find out my true transition state<br>
best regard<br>
<br>
<br>
<br>
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--0016e645ba42bbeac5046abfb521--
From owner-chemistry@ccl.net Mon May 25 19:01:01 2009
From: "Jim Kress ccl_nospam*_*kressworks.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Experimental and theratical UV calculation
Message-Id: <-39374-090525175355-17879-7roQBTiN/qsjs2fl/pDAYw**server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam,kressworks.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset="US-ASCII"
Date: Mon, 25 May 2009 17:48:07 -0400
MIME-Version: 1.0
Sent to CCL by: "Jim Kress" [ccl_nospam%a%kressworks.com]
An interesting new approach to calculating more of the detail David
mentioned is in the article by Taras Paetrenko and Frank Neese (
http://link.aip.org/link/?JCPSA6/127/164319/1 ) and is implemented in their
software, ORCA ( http://www.thch.uni-bonn.de/tc/orca/ ).
Jim
> -----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com]_[ccl.net
> [mailto:owner-chemistry+ccl_nospam==kressworks.com]_[ccl.net]
> On Behalf Of David Gallagher gallagher.da::gmail.com
> Sent: Monday, May 25, 2009 11:12 AM
> To: Kress, Jim
> Subject: CCL:G: Experimental and theratical UV calculation
>
> Hi Saurabh,
>
> There are various issues that can explain possible
> discrepancies between experimental and theoretical UV
> spectra, including geometry, solvation and vibrational fine
> structure, etc. The key issues are discussed and illustrated
> in a slide presentation posted at
> http://cacheresearch.com/presentations.html
> <http://cacheresearch.com/presentations.html> (top of page).
>
> I hope this helps.
> Regards,
> David Gallagher
> CACheResearch.com
>
>
> At 10:57 AM 5/23/2009, Saurabh Agrawal
> Saurabh.Agrawal!A!ucdconnect.ie wrote:
>
>
> Hello,
>
> I have calculated UV absorption spectrum for some
> molecules using Gaussian. With the following basis set and cards.
>
> #p B3LYP/6-31g** TD(Singlet,NSTATES=15) guess=read geom=check
>
> The results I got are considerably different from
> experimental results.
>
> 1) Can we compare the theoretical results with
> experimental results? I appreciate if some one could send
> link for some basic notes on it.
>
> Sincere regards,
>
> Saurabh
>
>
>
> Saurabh Agrawal,
> PhD Student,
> Department of Chemical and Bioprocess Engineering,
> UCD, Belfield,
> Dublin-4, Ireland
>
>