From chemistry-request@server.ccl.net Mon Oct 29 12:45:10 2001
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From: Robert Topper <roberttopper@roberttopper.com>
Cc: truhlar@chem.umn.edu, cramer@pollux.chem.umn.edu, sbachrach@trinity.edu,
   tuck@tosca.chem.nyu.edu, tcundari@memphis.edu, muguet@ensta.fr,
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Subject: ECCC8: Announce of Scientific Organizing Committee
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Dear colleagues and friends:

I am pleased to announce the Scientific Organizing Committee for ECCC8,
the 8th Electronic Computational Chemistry Conference, in March 2002
(http://eccc8.cooper.edu).

The following individuals have agreed to volunteer their time to help
organize the conference:

David Chatfield, Florida International University 
Tom Cundari, University of Memphis 
Walter Fabian,Karl-Franzens Universitaet Graz 
J.M.L. Martin, Weizmann Institute of Science (*)
Francis Muguet, E.N.S.Techniques Avancées (*)
Mark Tuckerman, New York University (*)

(*) = served on ECCC7 SOC

I am sure that everyone is most grateful for their service to the international computational chemistry community. We look forward to a successful meeting and encourage everyone to participate this year!

The ECCC8 URL is currently set up, so stay tuned to
http://eccc8.cooper.edu and the CCL for future announcements.

Robert Topper 
Principal Organizer, ECCC8 
topper@cooper.edu






From chemistry-request@server.ccl.net Tue Oct 30 11:07:30 2001
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Hi,

Anyone could tell me how to apply Eckart projection to project out the 3
independent translation and 3 rigid body rotaion from Hessian Matrix?
I mean how to write the 3N*6 Matrix C, so I can apply P=C*CT then
H'=PT*H*P.

Thanks.

Jun


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From: "Borosy, Andras {Basi~Basel}" <ANDRAS.BOROSY@Roche.COM>
Subject: program for lambda-max
To: chemistry@ccl.net
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Dear Colleauges,


Does anyone know a program for calculation (estimation) of maximum wavelengths of UV absorption (lambda-max). Other then Hyperchem.

Thanks,

András Borosy
Basilea Pharmaceutica Ltd
POB 3255, 65/316
4002 Basel
tel: +41-61-6885469
fax: +41-61-6882139
www.basileapharma.com


From chemistry-request@server.ccl.net Tue Oct 30 12:03:24 2001
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From: "Giorgio De Luca" <gio.deluca@unical.it>
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Subject: basis set procedure!!!
Date: Tue, 30 Oct 2001 18:10:33 +0100
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 Hi CCLers,
I have a question about Clementi procedure to optimize a basis set.
"Clementi" procedure optimizes the basis by "decontracting" a contracted =
basis set and using the SCF atomic coefficients without experimental =
atomic data, as reported in "Handbook of gaussian basis sets a =
compendium for ab-initio molecular orbital calculations".

do you know another Clementi procedure that uses experimental orbital =
energies or
experimental atomic data but still uses  the SCF atomic coefficients to =
define the contraction coefficients.
Thank you in advance.
G. De luca.
 =20

------=_NextPart_000_0100_01C1616E.2B092140
Content-Type: text/html;
	charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META content=3D"text/html; charset=3Diso-8859-1" =
http-equiv=3DContent-Type>
<META content=3D"MSHTML 5.00.2614.3500" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>&nbsp;<FONT size=3D2>Hi =
CCLers,</FONT></FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I have a question about Clementi =
procedure to=20
optimize a basis set.</FONT></DIV>
<DIV><FONT size=3D2><FONT face=3DArial>"Clementi" procedure optimizes =
the basis by=20
"decontracting" a contracted basis set and using the SCF atomic =
coefficients=20
without experimental atomic data, as reported in <FONT =
face=3DArial>"Handbook of=20
gaussian basis sets</FONT><FONT face=3DArial> a compendium for ab-initio =
molecular=20
orbital calculations".</FONT></FONT></FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>do you know another Clementi procedure =
that uses=20
experimental orbital energies or</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>experimental atomic data&nbsp;but=20
still&nbsp;uses&nbsp; the&nbsp;SCF&nbsp;atomic coefficients to define=20
the&nbsp;contraction coefficients.</FONT></DIV>
<DIV><FONT face=3DArial>
<DIV><FONT face=3DArial size=3D2>Thank you in advance.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>G. De luca.</FONT></DIV>
<DIV><FONT face=3DArial></FONT><FONT size=3D2>&nbsp;</FONT></FONT><FONT=20
size=3D2>&nbsp;</FONT></DIV></DIV></BODY></HTML>

------=_NextPart_000_0100_01C1616E.2B092140--



From chemistry-request@server.ccl.net Tue Oct 30 14:36:09 2001
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Date: Tue, 30 Oct 2001 14:08:32 -0500
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Subject: Re: CCL:program for lambda-max
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Hi all

Won't Chem2Pac do this?  I believe that it calculates absorption spectra from a Mopac
output.

Richard


"Borosy, Andras {Basi~Basel}" wrote:

> Dear Colleauges,
>
> Does anyone know a program for calculation (estimation) of maximum wavelengths of UV absorption (lambda-max). Other then Hyperchem.
>
> Thanks,
>
> András Borosy
> Basilea Pharmaceutica Ltd
> POB 3255, 65/316
> 4002 Basel
> tel: +41-61-6885469
> fax: +41-61-6882139
> www.basileapharma.com
>
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
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> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
Post-doctoral Associate
Department of Food Science
120 Stocking Hall
Cornell University, Ithaca, NY 14853





From chemistry-request@server.ccl.net Tue Oct 30 23:05:11 2001
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From: "Elena Jakubikova" <immina@hotmail.com>
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Subject: Gaussian calculation speed
Date: Tue, 30 Oct 2001 21:08:09 -0700
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Dear CCLers,

I have run one CISD calculation with a relatively large
basis set on CH4 molecule on 2 different computers.
Computer one is Dell 550MHz Pentium III, 512MB RAM
(100MHz SDRAM), 18 GB SCSI #1 Hard Drive, and Red Hat
Linux 6.0 operating system. Computer two is Millennia
733MHz Pentium III, 770MB RAM (133MHz SDRAM), 27GB IDE
ATA-66 hard drive, and Red Hat Linux 7.0 operating
system.
To my big surprise the calculation was much faster on
Dell (job cpu time = 24 minutes 1.8 sec) than on
Millennia (job cpu time = 1 hour 4 minutes 18.6
seconds). The output files I got from these computers
were completely identical, except the time gaussian spent
executing each link. Millennia computer took less time in
almost all cases (as one would expect from computer
specifications), except Link 401 (forms initial MO
guess), Link 804 (integral transformation), and Link 913
(calculates post SCF energies and gradient terms), where
Dell computer was much faster.
I tried to run top while running only this one
calculation and found out that during the extensive I/O
phase of calculation (l804,l913), there is a lot of CPU
used by the system on Millennia computer (at certain
moments its more than 90%), whereas in the case of Dell
computer almost all cpu is used by the user.
I am very puzzled by this results - Millennia computer
appears to be better suited for calculations, but it is
about 3 times slower. I wonder if this result is a
software issue that can be easily fixed or it is some
hardware problem. I would be very grateful to anybody who
has any ideas what is causing this result.

Thank you

Elena Jakubikova
graduate student
Colorado State University

_________________________________________________________________
Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp



From chemistry-request@server.ccl.net Tue Oct 30 21:21:50 2001
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Dear all:

I posted sometime ago a question on CCL about electronegativities on UFF.  I
got two answers and requests for summary.  Apparently there is not much
clarity about this, however I believe, the answers I got pretty much cover
the topic, besides solving my particular problem:-).  I will be interested
however if someone else follows this topic.  I'll send out to interested
people anything else I can found.

Thank you to Dr. Senn again, his thesis has all I (and probably anybody
else) needed about UFF, if you have a question about UFF you might want to
first take a look to sect. 2.7.3 in his thesis.
(full text at http://e-collection.ethbib.ethz.ch/show?type=diss&nr=13972),
Sect. 2.7.3.

Thank you also to Dr. Bronwyn Thomas.  I actually looked for the paper he
pointed out but only electronegativity for a few atoms are shown sending the
reader to a reference submitted for publication, which, as happened to Dr.
Senn I could not find.  The electronegativity is however defined in the
paper pointed by Dr. Thomas and a full table of Generalized Pauling-Mulliken
electronegativities can be found in Dr. Senn Thesis.

Please see below the full answers and well at the bottom the original
question.

Thanks,

Pedro

***********************************************************************
Referring to your recent question sent to the CCL about the
electronegativities:
Another flaw of Rappé's paper; he refers to his "GMP
electronegativities" as submitted for publication, but the paper
never came out...

Back when I was doing it, Mark Thompson posted the same question to
the CCL (you should even be able to dig it out of the list archive).
He is the guy who wrote ArgusLab (http://www.planaria-software.com/),
which includes an UFF implementation. So I asked him to keep me
updated about the issue.
He finally got the GMP electronegativities directly from Rappé upon
request and forwarded them to me. That's why I referenced Table 2.2
in my thesis as personal communication from Rappé. At the time, Mark
told me that Rappé had told him he would put these values on the web.
Which never happened, I suppose...

Cheers,

Hans

*************************************************************************
These electronegativities are in eV. They have been calculated by Rappe and
Goddard - see J. Phys. Chem. 95, 3358-63 (1991), where some of these values
are reported. Nominally, they are calculated as the average of the
ionisation potential and the electron affinity (in eV).

However, some care should be taken when using these values, I have found.
Check that the quoted electronegativity does reflect the most recent values
of ionisation potential and electron affinity. Hydrogen is a bit of a
different case - see the paper mentioned above.

regards,
Bronwyn Thomas.

****************************************************************************
****************************************************************************
ORIGINAL QUESTION

> Dear all:
>
>         I have another question about Universal Force Field 1.02 as
> implemented in Cerius2.  Do any of you know which unit are used for the
> electronegativity?, According to Cerius they are in Pauling which is
> obviously not correct since several of them are larger than 4.  They seems
> to be in eV, for example UFF1.02 value for Li is 3.006 while according to
> one of my references (Density-Functional Theory of Atoms and Molecules, by
> Parr and Yang) this value is 3.01 which is given in eV.
>
> Other values agree fairly well, F(UFF1.02)=10.874 vs. F(Parr)=10.41 eV.
>
> But other values are awfully different like for example H(UFF1.02)=4.528,
> H(Parr)=7.18 eV, or Cu(UFF1.02)=3.729 while Cu(Parr)=4.48 eV.
>
> Is this different due to a parameterization obtain in different experiment
> or they are really given in a different unit.
>
> Thank you for your help
>
> Pedro
>





From chemistry-request@server.ccl.net Tue Oct 30 16:39:21 2001
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Reply-To: "Mark A. Thompson" <markt158@home.com>
From: "Mark A. Thompson" <markt158@home.com>
To: "Borosy, Andras {Basi~Basel}" <ANDRAS.BOROSY@Roche.COM>,
   <chemistry@ccl.net>
References: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA7D3@rbamsem3.bas.roche.com>
Subject: Re: CCL:program for lambda-max
Date: Tue, 30 Oct 2001 13:39:28 -0800
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Yes, ArgusLab will do these calculations.
You can obtain ArgusLab 2.0 for free from:
http://www.planaria-software.com

In addition to spectra, ArgusLab has a great 3D molecule builder and
supports a variety of other computational methods, including UFF for the
whole periodic table.

Mark


----- Original Message -----
From: "Borosy, Andras {Basi~Basel}" <ANDRAS.BOROSY@Roche.COM>
To: <chemistry@ccl.net>
Sent: Tuesday, October 30, 2001 7:40 AM
Subject: CCL:program for lambda-max


> Dear Colleauges,
>
>
> Does anyone know a program for calculation (estimation) of maximum
wavelengths of UV absorption (lambda-max). Other then Hyperchem.
>
> Thanks,
>
> András Borosy
> Basilea Pharmaceutica Ltd
> POB 3255, 65/316
> 4002 Basel
> tel: +41-61-6885469
> fax: +41-61-6882139
> www.basileapharma.com
>
>
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To
Admins
> MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
> CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net
70
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan:
jkl@ccl.net
>
>
>
>
>
>