From owner-chemistry@ccl.net Sun Mar 30 07:19:01 2008
From: "Jerome Kieffer jerome.Kieffer#terre-adelie.org" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL:G: emission spectrum
Message-Id: <-36587-080330064939-18585-djHQ9ISeOlAZ8QJvKJTNnQ=server.ccl.net>
X-Original-From: Jerome Kieffer <jerome.Kieffer^terre-adelie.org>
Content-Transfer-Encoding: quoted-printable
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Date: Sun, 30 Mar 2008 12:51:04 +0200
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Sent to CCL by: Jerome Kieffer [jerome.Kieffer#terre-adelie.org]
> Could you please tell me how could I simulate the emission spectrum of a =
system with Gaussian03? Exactly what commands should I include in the route=
section in order to do this with TDDFT and CIS? In addition, could I have =
the emission spectrum using GaussSum? In the G03 manual it is not clear how=
one can study the S1 instead of S0 state with TDDFT or CIS. What commands =
should be included in the route section (td(Root=3D1)?)
Hello,
I think this is really difficult as S1 state generated by photo
excitation (or whatever) will relax and there are little tools to allow
geometry optimization of the exitated state (no analytic gradients in
TDDFT).
I could be wrong ... thus very interested by the solution.
Reagards
--=20
J=E9r=F4me KIEFFER : http://www.terre-adelie.org
From owner-chemistry@ccl.net Sun Mar 30 10:39:00 2008
From: "Niklas Loges niklas.loges=-=web.de" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Computing Raman spectra for crystalline inorganics
Message-Id: <-36588-080330103732-31404-yRCj2oqtxZrD5sIMAf7XCA===server.ccl.net>
X-Original-From: "Niklas Loges" <niklas.loges^web.de>
Date: Sun, 30 Mar 2008 10:37:28 -0400
Sent to CCL by: "Niklas Loges" [niklas.loges_-_web.de]
Hello,
does someone know a program (an open source/freeware program would be preferred) which can calculate Raman spectra from inorganic crystalline substances?
Cheers,
Niklas
--
Dipl. Chem. Niklas Loges
Johannes Gutenberg-Universitt
Institut fr Anorganische und Analytische Chemie
Arbeitskreis Prof. W. Tremel
Forschung Sd, Raum 03-114
Duesbergweg 10-14
55099 Mainz
Tel.: (06131) 39-23920
From owner-chemistry@ccl.net Sun Mar 30 12:35:01 2008
From: "Mireille Krier mv.krier(a)googlemail.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Graphics demos
Message-Id: <-36589-080329070041-23760-gZpXEmPpgqrQNFY3DBy5tQ|-|server.ccl.net>
X-Original-From: "Mireille Krier" <mv.krier/a\googlemail.com>
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Date: Sat, 29 Mar 2008 11:04:17 +0100
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Sent to CCL by: "Mireille Krier" [mv.krier:googlemail.com]
------=_Part_36050_3713851.1206785057105
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Dear John,
there is a really cool software called YASARA
http://www.yasara.org
The tutorials are really instructive and self-explanatory.
I don't know Elmar Krieger personnally, but I was told that he was
programming for the gaming industry before; so you will understand why the
graphics look so great and are optimized for speed.
Cheers,
Mireille
On 3/28/08, John McKelvey jmmckel##gmail.com <owner-chemistry*|*ccl.net>
wrote:
>
> Folks,
>
> I am giving a seminar on applications of theory in industry. Now I have
> done this many times in the past, mostly to undergrad and grad students who
> are comfortable with theory, though in varying degrees. The next challenge
> is to give one in an undergraduate department where theory in detail is not
> appropriate, but I can give some black box descriptions of methods and
> results. What would be nice, I'm told, would be some appropriate "cool
> graphics." I'm not strong in the bio/pharma area, but do understand a bit
> of the importance of docking, etc. Demoing some dynamics results on a
> simple reaction could be interesting, for example.
>
> I'm most receptive to any and all suggestions, and any demos that might be
> available..
>
> Many thanks!!
>
> John McKelvey
>
------=_Part_36050_3713851.1206785057105
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit
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<div>Dear John,</div>
<div> </div>
<div>there is a really cool software called YASARA</div>
<div><a href="http://www.yasara.org/">http://www.yasara.org</a><br>The tutorials are really instructive and self-explanatory. </div>
<div>I don't know Elmar Krieger personnally, but I was told that he was programming for the gaming industry before; so you will understand why the graphics look so great and are optimized for speed.</div>
<div>Cheers,</div>
<div> </div>
<div>Mireille</div>
<div><br> </div>
<div><span class="gmail_quote">On 3/28/08, <b class="gmail_sendername">John McKelvey jmmckel##gmail.com</b> <<a href="mailto:owner-chemistry*|*ccl.net">owner-chemistry*|*ccl.net</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Folks,<br><br>I am giving a seminar on applications of theory in industry. Now I have done this many times in the past, mostly to undergrad and grad students who are comfortable with theory, though in varying degrees. The next challenge is to give one in an undergraduate department where theory in detail is not appropriate, but I can give some black box descriptions of methods and results. What would be nice, I'm told, would be some appropriate "cool graphics." I'm not strong in the bio/pharma area, but do understand a bit of the importance of docking, etc. Demoing some dynamics results on a simple reaction could be interesting, for example. <br>
<br>I'm most receptive to any and all suggestions, and any demos that might be available..<br><br>Many thanks!!<br><span class="sg"><br>John McKelvey<br></span></blockquote></div><br>
------=_Part_36050_3713851.1206785057105--
From owner-chemistry@ccl.net Sun Mar 30 13:14:00 2008
From: "Geoffrey Hutchison geoffh|pitt.edu" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Graphics demos
Message-Id: <-36590-080330111336-18458-1nYrv+Wws5NRaONsh6WrNw _ server.ccl.net>
X-Original-From: Geoffrey Hutchison <geoffh.:.pitt.edu>
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Date: Sun, 30 Mar 2008 10:40:31 -0400
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Sent to CCL by: Geoffrey Hutchison [geoffh:_:pitt.edu]
> The next challenge is to give one in an undergraduate department
> where theory in detail is not appropriate, but I can give some black
> box descriptions of methods and results. What would be nice, I'm
> told, would be some appropriate "cool graphics."
I'm not the right person for reaction paths or docking -- both of
those would be excellent for such a talk.
I have gotten a lot of interest from showing simple things:
* A live geometry optimization using molecular mechanics -- the
molecule "pops" from a bad initial geometry into a better one and then
continues to "squirm" (actual quotes).
* Conformational / rotor searching on a larger molecule -- showing how
different conformers are sampled to find the local minima.
* Molecular dynamics
Animations of molecular vibrations and even simple pictures of
molecular orbitals are often interesting for undergraduates.
Maybe we need to get some animations like this onto CCL.net or
YouTube. (The latter has some great experimental demos, so why not
theory?)
Cheers,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh---pitt.edu
web: http://hutchison.chem.pitt.edu/
From owner-chemistry@ccl.net Sun Mar 30 13:45:00 2008
From: "John McKelvey jmmckel .. gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL:G: emission spectrum
Message-Id: <-36591-080330124850-12363-ewP6+t5sa4wd4z+6VdIvMg]*[server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel+*+gmail.com>
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There are analytical first, and I think analytical second derivatives, for
CIS in Gaussian.
Also, there are analytical first derivatives for TDDFT in TURBOMOLE.
Cheers,
John McKelvey.
On Sun, Mar 30, 2008 at 6:51 AM, Jerome Kieffer
jerome.Kieffer#terre-adelie.org <owner-chemistry[a]ccl.net> wrote:
>
> Sent to CCL by: Jerome Kieffer [jerome.Kieffer#terre-adelie.org]
>
> > Could you please tell me how could I simulate the emission spectrum of =
a
> system with Gaussian03? Exactly what commands should I include in the rou=
te
> section in order to do this with TDDFT and CIS? In addition, could I have
> the emission spectrum using GaussSum? In the G03 manual it is not clear h=
ow
> one can study the S1 instead of S0 state with TDDFT or CIS. What commands
> should be included in the route section (td(Root=3D1)?)
>
> Hello,
> I think this is really difficult as S1 state generated by photo
> excitation (or whatever) will relax and there are little tools to allow
> geometry optimization of the exitated state (no analytic gradients in
> TDDFT).
>
> I could be wrong ... thus very interested by the solution.
>
> Reagards
>
> --
> J=E9r=F4me KIEFFER : http://www.terre-adelie.org
>
>
>
> - This is automatically added to each message by the mailing script ->
>
>
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Content-Disposition: inline
There are analytical first, and I think analytical second derivatives, for =
CIS in Gaussian.<br><br>Also, there are analytical first derivatives for TD=
DFT in TURBOMOLE.<br><br>Cheers,<br><br>John McKelvey.<br><br><div class=3D=
"gmail_quote">
On Sun, Mar 30, 2008 at 6:51 AM, Jerome Kieffer jerome.Kieffer#terre-adelie=
.org <<a href=3D"mailto:owner-chemistry[a]ccl.net">owner-chemistry[a]ccl.net=
</a>> 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: Jerome Kieffer [jerome.Kieffer#terre-adelie.org]<br>
<br>
> Could you please tell me how could I simulate the emission spectrum of=
a system with Gaussian03? Exactly what commands should I include in the ro=
ute section in order to do this with TDDFT and CIS? In addition, could I ha=
ve the emission spectrum using GaussSum? In the G03 manual it is not clear =
how one can study the S1 instead of S0 state with TDDFT or CIS. What comman=
ds should be included in the route section (td(Root=3D1)?)<br>
<br>
Hello,<br>
I think this is really difficult as S1 state generated by photo<br>
excitation (or whatever) will relax and there are little tools to allow<br>
geometry optimization of the exitated state (no analytic gradients in<br>
TDDFT).<br>
<br>
I could be wrong ... thus very interested by the solution.<br>
<br>
Reagards<br>
<br>
--<br>
J=E9r=F4me KIEFFER : <a href=3D"http://www.terre-adelie.org" target=
=3D"_blank">http://www.terre-adelie.org</a><br>
<br>
<br>
<br>
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</blockquote></div><br>
------=_Part_2955_24363682.1206895699380--
From owner-chemistry@ccl.net Sun Mar 30 14:29:00 2008
From: "John McKelvey jmmckel:_:gmail.com" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: Graphics demos
Message-Id: <-36592-080330142445-12517-JlIneMCaW8AOmX7tfEcuhw . server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel*gmail.com>
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Date: Sun, 30 Mar 2008 14:24:28 -0400
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Sent to CCL by: "John McKelvey" [jmmckel : gmail.com]
------=_Part_3303_18439128.1206901468900
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Dear Mireille,
this looks quite interesting.
Best regards, and many thanks,
John
On Sat, Mar 29, 2008 at 6:04 AM, Mireille Krier mv.krier(a)googlemail.com <
owner-chemistry%%ccl.net> wrote:
> Dear John,
>
> there is a really cool software called YASARA
> http://www.yasara.org
> The tutorials are really instructive and self-explanatory.
> I don't know Elmar Krieger personnally, but I was told that he was
> programming for the gaming industry before; so you will understand why the
> graphics look so great and are optimized for speed.
> Cheers,
>
> Mireille
>
>
> On 3/28/08, John McKelvey jmmckel##gmail.com <owner-chemistry(-)ccl.net<owner-chemistry%28-%29ccl.net>>
> wrote:
> >
> > Folks,
> >
> > I am giving a seminar on applications of theory in industry. Now I have
> > done this many times in the past, mostly to undergrad and grad students who
> > are comfortable with theory, though in varying degrees. The next challenge
> > is to give one in an undergraduate department where theory in detail is not
> > appropriate, but I can give some black box descriptions of methods and
> > results. What would be nice, I'm told, would be some appropriate "cool
> > graphics." I'm not strong in the bio/pharma area, but do understand a bit
> > of the importance of docking, etc. Demoing some dynamics results on a
> > simple reaction could be interesting, for example.
> >
> > I'm most receptive to any and all suggestions, and any demos that might
> > be available..
> >
> > Many thanks!!
> >
> > John McKelvey
> >
>
>
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Dear Mireille,<br><br>this looks quite interesting. <br><br>Best regards, and many thanks,<br><br>John<br><br><div class="gmail_quote">On Sat, Mar 29, 2008 at 6:04 AM, Mireille Krier mv.krier(a)googlemail.com <<a href="mailto:owner-chemistry%%ccl.net">owner-chemistry%%ccl.net</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Dear John,</div>
<div> </div>
<div>there is a really cool software called YASARA</div>
<div><a href="http://www.yasara.org/" target="_blank">http://www.yasara.org</a><br>The tutorials are really instructive and self-explanatory. </div>
<div>I don't know Elmar Krieger personnally, but I was told that he was programming for the gaming industry before; so you will understand why the graphics look so great and are optimized for speed.</div>
<div>Cheers,</div>
<div> </div>
<div>Mireille</div>
<div><br> </div>
<div><span class="gmail_quote">On 3/28/08, <b class="gmail_sendername">John McKelvey jmmckel##gmail.com</b> <<a href="mailto:owner-chemistry%28-%29ccl.net" target="_blank">owner-chemistry(-)ccl.net</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Folks,<br><br>I am giving a seminar on applications of theory in industry. Now I have done this many times in the past, mostly to undergrad and grad students who are comfortable with theory, though in varying degrees. The next challenge is to give one in an undergraduate department where theory in detail is not appropriate, but I can give some black box descriptions of methods and results. What would be nice, I'm told, would be some appropriate "cool graphics." I'm not strong in the bio/pharma area, but do understand a bit of the importance of docking, etc. Demoing some dynamics results on a simple reaction could be interesting, for example. <br>
<br>I'm most receptive to any and all suggestions, and any demos that might be available..<br><br>Many thanks!!<br><span><br>John McKelvey<br></span></blockquote></div><br>
</blockquote></div><br>
------=_Part_3303_18439128.1206901468900--
From owner-chemistry@ccl.net Sun Mar 30 15:15:01 2008
From: "Istvan Mayer mayer*o*chemres.hu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: New free programs
Message-Id: <-36593-080330125238-13971-GIGYuCzkC9DeCGTO9S4Nrw-#-server.ccl.net>
X-Original-From: Istvan Mayer <mayer(0)chemres.hu>
Date: Sun, 30 Mar 2008 19:16:27 +0200
Sent to CCL by: Istvan Mayer [mayer:chemres.hu]
Dear CCL-ers,
this is to inform you that several new programs have been put on our
web-site
http://occam.chemres.hu
and may be freely downloaded, similarly to the other programs there. (Some
minor bugs of older programs have also been corrected.) Most of these
programs are devoted to post-processing of the results obtained in a
Gaussian run - for other program-systems the interfacing should be solved.
The new programs are:
1. Program CIS-T
A program permitting to present the results of a CIS, TD-HF or TD-DFT
calculation in a maximally compact form by using the "singular value
decomposition" algorithm, and to obtain the natural orbitals of the
excited states, characterizing the electron excitations of the individual
chromophores. The visualization of these orbitals can also be made - e.g.
by invoking the MOLDEN program.
The algorithms are described in I. Mayer, Chem. Phys. Letters 437, 284
(2007) and ibid. 443, 420 (2007). The program utilizes the Gaussian output
file only, and also produces a copy of latter with the modified orbitals
inserted.
2. Program ENPART (Former HFx)
a) Bond order and valence calculation according to I. Mayer, Chem. Phys.
Letters 97, 270 (1083) etc.
b) Decomposition of the HF energy (closed shells) into atomic and diatomic
components according to the schemes discussed in I. Mayer, Phys. Chem.
Chem. Phys. 8, 4630 (2006).
3. Program BO-SPIN
a) Bond order and valence calculation according to I. Mayer, Chem. Phys.
Letters 97, 270 (1983), for open shells IJQC 26, 73 (1986), etc.
b) Decomposition of the <S**2> expectation value into atomic and diatomic
components according to the scheme described in I. Mayer, Chem. Phys.
Letters 440, 357 (2007).
That is useful to identify local spins (e.g. on transition metals)
which can be obtained in the UHF framework.
The program is applicable for large systems (up to 2000 orbitals) and
can easily be extended further.
Programs ENPART and BO-SPIN use my original bond order routine of 1982/83
and some routines from the program APOST by I. Mayer and A. Hamza
(Budapest, 2000). They require only a formatted checkpoint file produced
in a Gaussian run (G92...G03).
Please send any remarks and questions to the e-mail mayer,+,chemres.hu.
Istvan Mayer
--------------------------------------------------
Prof. Istvan Mayer
Chemical Research Center
Hungarian Academy of Sciences
H-1525 Budapest, P.O.Box 17, Hungary
Phone: (+361) 438-41-41, -42...-45 (ext. 295, 107)
Fax: (+361) 438-1143, 438-1142, 325-7554, 325-7750
e-mail: mayer,+,chemres.hu
---------------------------------------------------
From owner-chemistry@ccl.net Sun Mar 30 18:31:01 2008
From: "kcousins:-:csusb.edu" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Graphics demos
Message-Id: <-36594-080330151242-9942-1vdQ3j5UzuFP7IxXoX+Q5w(_)server.ccl.net>
X-Original-From: kcousins!^!csusb.edu
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Date: Sun, 30 Mar 2008 11:11:45 -0700
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Sent to CCL by: kcousins===csusb.edu
H Geoffey et al.
There are already some interesting molecular graphics, including binding, docking, mechanics, etc. on Youtube.com
What would be interesting to develop is a "guide" for educators and speakers, as to the science behind these visualizations (as well as the validity of each). There are "comments" than can be added to Youtube videos by joining youtube (no cost). Or an external guide could be developed . . .
Kimberley R. Cousins
Professor of Chemistry
California State University, San Bernardino
http://chem.csusb.edu/~kcousins
kcousins###csusb.edu
----- Original Message -----
> From: "Geoffrey Hutchison geoffh|pitt.edu" <owner-chemistry###ccl.net>
Date: Sunday, March 30, 2008 10:56 am
Subject: CCL: Graphics demos
To: "Cousins, Kimberley " <kcousins###csusb.edu>
>
> Sent to CCL by: Geoffrey Hutchison [geoffh:_:pitt.edu]
> > The next challenge is to give one in an undergraduate department
> > where theory in detail is not appropriate, but I can give some
> black
> > box descriptions of methods and results. What would be nice, I'm
>
> > told, would be some appropriate "cool graphics."
>
>
> I'm not the right person for reaction paths or docking -- both of
> those would be excellent for such a talk.
>
> I have gotten a lot of interest from showing simple things:
> * A live geometry optimization using molecular mechanics -- the
> molecule "pops" from a bad initial geometry into a better one and
> then
> continues to "squirm" (actual quotes).
> * Conformational / rotor searching on a larger molecule -- showing
> how
> different conformers are sampled to find the local minima.
> * Molecular dynamics
>
> Animations of molecular vibrations and even simple pictures of
> molecular orbitals are often interesting for undergraduates.
>
> Maybe we need to get some animations like this onto CCL.net or
> YouTube. (The latter has some great experimental demos, so why not
> theory?)
>
> Cheers,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geoffh:pitt.edu
> web: http://hutchison.chem.pitt.edu/
>
>
>
> -= This is automatically added to each message by the mailing
> script =-
> To recover the email address of the author of the message, please
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> also> Conferences:
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>
>