From chemistry-request@ccl.net Mon Jun 21 03:32:05 2004
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From: "Noel O'Boyle" <noel.oboyle2<<at>>mail.dcu.ie>
Subject: RE: CCL:Freq calculation error in G03
To: "Ian Hovell" <HOVELL<<at>>cetem.gov.br>
Cc: chemistry<<at>>ccl.net
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Hello Ian,

Gaussian is very particular about blank lines. You need two blank lines
after the route (#) section. Don't ask me why.

So it should be something like this:
# freq=(noraman,readiso,readfc) ub3lyp/6-31+g(d) geom=Allcheck
 
298.15 1.0 0.9806
14.00307
12.00000
12.00000
12.00000
12.00000
12.00000
1.00783
1.00783
(end of file)

I am not sure if you need to include the isomer section, but it's no harm
to include it if it still doesn't work for you. You can take the values
> from your frequency calculation output file using the following Linux command:

gawk '/has atomic number/ {print $9}' freqcalc.out >> input.gjf

Noel

>-- Original Message --
>From: Ian Hovell <HOVELL<<at>>cetem.gov.br>
>To: "'chemistry'" <chemistry<<at>>ccl.net>
>Subject: CCL:Freq calculation error in G03
>Date: Fri, 18 Jun 2004 16:24:53 -0300
>
>
>Dear CCLers,
>
>I have carried out the following frequency calculation in G98w without
>problems. But on using G03 on the same computer I get the following error.
>Any suggestions would be extremely welcome and a summary of the replies
will
>appear.
>
>The molecule is optimised and a frequency calculation is performed and
then
>repeated in a second job which scales the frequencies at 298K The 2 lines
>I
>use to perform this second job are:-
>
># freq=(noraman,readiso,readfc) ub3lyp/6-31+g(d) geom=Allcheck
> 
>298.15 1.0 0.9806
>end of job file
>
>The edited result from G03 is shown below.
>
> Recover connectivity data from disk.
>  WANTED A FLOATING POINT NUMBER AS INPUT.
>  FOUND A STRING AS INPUT.
> Atom number 3, atomic number 1: [1]
>
> 
>
>?
> Error termination via Lnk1e 
>
>
>Ian Hovell - Ph.D. 
>NUCLEO DE MODELAGEM MOLECULAR-NMM 
>Centro de Tecnologia Mineral - CETEM 
>Ministerio da Cijncia e da Tecnologia- MCT 
>Avenida Ipj, No 900 - Cidade Universitaria 
>Ilha do Fundco Rio de Janeiro RJ Brasil 
>CEP 21941-590 
>tel 00 55 (xx) 3865 7344 ou 3865 - 7216 
>Fax 00 55 (xx) 22602837 ou 2290-4286 
>e-mail hovell<<at>>cetem.gov.br <mailto:hovell<<at>>cetem.gov.br>  
>
>
>
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From chemistry-request@ccl.net Mon Jun 21 11:44:01 2004
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From: "Irena Efremenko" <chrirena-.at.-techunix.technion.ac.il>
To: "ccl" <chemistry-.at.-ccl.net>
Subject: NBO in Gaussian
Date: Mon, 21 Jun 2004 19:50:13 +0200
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Dear CCLers,

I have sevaral questions about NBO implementation in Gaussian. I work =
with G03 but G98 shows the same features.

1. NBO analysis of the Cu2 dimer with effective core potential performed =
in G03 at exactly the same level of theory as that in the NBO 4.m =
program manual provides completely different results. Particularly, G03 =
gives only one bonding (BD) and one antibonding (BD*) orbitals while the =
manual lists 3 orbitals of each kind.=20

2. The "$nbo keyword(s) $end" section recommended in G03 manual is =
ignored by the program.=20
=20
3. The second job step performed according to the G03 manual in order to =
place the natural orbitals into the checkpoint file:

--Link1--=20
%Chk=3Dname=20
# Guess=3D(Read,Save,Only,NaturalOrbitals) Geom=3DAllCheck

leads to the error message saying that orbital information is not in the =
read-write file.

4. If I cannot save orbital information in the checkpoint file and =
cannot use "$nbo plot" option, how can I see NBO orbitals (using Molden, =
Molekel, ArgusLab, gOpenMol, GaussView)?

5. To what extend NBO 4.M program manual could be applied with Gaussian?

Any suggestions will be appreciated.

---------------
Dr. Irena Efremenko
Wolfson Department of Chemical Engineering
Technion - Israel Institute of Technology
Haifa 32000, Israel
Phone: 972-4-8293561
Fax: 972-4-8295672
------=_NextPart_000_09C7_01C457C8.F7785270
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	charset="windows-1255"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Dwindows-1255">
<META content=3D"MSHTML 6.00.2800.1400" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear CCLers,<BR></FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I have sevaral questions about NBO =
implementation=20
in Gaussian. I work with G03 but G98 shows the same =
features.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>1. NBO analysis of the Cu2 dimer with =
effective=20
core potential performed in G03 at exactly the same level of theory as =
that in=20
the NBO 4.m program manual provides completely different results. =
Particularly,=20
G03 gives only one bonding (BD) and one antibonding (BD*) orbitals while =
the=20
manual lists 3 orbitals of each kind. </FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>2. The "$nbo&nbsp;keyword(s) $end" =
section=20
recommended in G03 manual is ignored by the=20
program.&nbsp;<BR>&nbsp;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>3.&nbsp;The second job step performed =
according to=20
the G03 manual in order to place the natural orbitals into the =
checkpoint=20
file:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>--Link1-- <BR>%Chk=3D<I>name</I> <BR>#=20
Guess=3D(Read,Save,Only,NaturalOrbitals) Geom=3DAllCheck</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>leads to the error message saying that =
orbital=20
information is not in the read-write file.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>4. If I cannot save orbital information =
in the=20
checkpoint file and cannot use "$nbo plot" option, how can I see NBO =
orbitals=20
(using Molden, Molekel, ArgusLab, gOpenMol, GaussView)?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>5. To what extend NBO 4.M program =
manual&nbsp;could=20
be applied with Gaussian?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Any suggestions will be =
appreciated.</FONT></DIV>
<DIV><FONT face=3DArial><FONT size=3D2>&nbsp;</DIV></FONT></FONT>
<DIV><FONT face=3DArial size=3D2>---------------<BR>Dr. Irena =
Efremenko<BR>Wolfson=20
Department of Chemical Engineering<BR>Technion - Israel Institute of=20
Technology<BR>Haifa 32000, Israel<BR>Phone: 972-4-8293561<BR>Fax:=20
972-4-8295672</FONT></DIV></BODY></HTML>

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From chemistry-request@ccl.net Mon Jun 21 09:28:49 2004
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Subject: RE: Re[2]: how to calculate proton dissociation energy in GAUSSIAN03
Date: Mon, 21 Jun 2004 10:32:15 -0400
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Thread-Topic: Re[2]: how to calculate proton dissociation energy in GAUSSIAN03
Thread-Index: AcRV6zpuzdUrojjtSMmhqWnPePKgMABsEysg
From: "Shobe, David" <dshobe-.at.-sud-chemieinc.com>
To: "Qiang Lu" <qiangl-.at.-uci.edu>, "Errol Lewars" <elewars-.at.-trentu.cA>
Cc: <chemistry-.at.-ccl.net>
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Qiang,

The energy of H+ is exactly zero at zero K.  At room temperature there is a slight contribution from translational energy.  It's a simple formula, E = (3/2)kT, k=Boltzmann's constant, T = absolute temperature.

--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.


-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request-.at.-ccl.net]On
Behalf Of Qiang Lu
Sent: Friday, June 18, 2004 9:59 PM
To: Errol Lewars
Cc: chemistry-.at.-ccl.net
Subject: CCL:Re[2]: how to calculate proton dissociation energy in
GAUSSIAN03


Hi Errol,

Thank you for you reply. That is what I mean. And for the energy of
H+, can I simply do a single point calculation of H+?

-- 
Best regards,
 Qiang                            mailto:qiangl-.at.-uci.edu


=================Original message text===============
Hello,

You mean deltaE for the reaction BH --> B- + H+  , where BH is imidazole 
coordinated to Zn++?
You calculate the energy of the optimized structure BH, and the energy 
of the optimized B-, and take the difference in E of the of thr reactant 
and the products. The level of the calc may be mnportant, so work your 
way up.

EL
===


Qiang Lu wrote:

>Dear CCL-ers,
>
>I want to calculate the proton dissociation energy of imidazole when
>it is a ligand of ZN. Could you tell me some hint about how to perform
>it? Any suggestion will be helpful. Thank you in advance.
>
>  
>
>  
>

==============End of original message text===========



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From chemistry-request@ccl.net Mon Jun 21 10:13:42 2004
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Date: Mon, 21 Jun 2004 17:19:53 +0200
From: Marc Noguera Julian <marc[at]klingon.uab.es>
Subject: AMD 64, AMD 64 FX, and opteron.
To: chemistry[at]ccl.net
Message-id: <40D6FC99.6080604[at]klingon.uab.es>
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Hello,
I am having some trouble discovering the differences between opteron, 
AMD 64 and AMD 64 FX processors.
Are they so subtle?
Any ideas?
Marc


From chemistry-request@ccl.net Mon Jun 21 13:09:54 2004
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From: James Robinson <prsjjr(at)bath.ac.uk>
To: CHEMISTRY(at)ccl.net
Subject: rates of reaction in solution phase
Date: Mon, 21 Jun 2004 19:14:30 +0100
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Dear CCLers

Having calculated the PES for a reaction and being able to extract Free energy data from frequency calculations, one can calculate a rate of reaction using either Arrhenius and/or Eyring equation. However, I have found that PCM/B3LYP calculations give me very high rates of reaction using the Eyring equation when applied to a reaction in solution, hardly suprising. 

How does one apply diffusion and/or viscoity corrections to obtain more realistic values. I am using G98 revision A.6, running on sgi origin. I have read through books by Hirschfelder et al, Pearson and Frost. I can find no simple empirical corrections. 

I have found CPCM/B3LYP calcs give nice values for calculating pka, but even this data gives very high rate of reaction for solution phase reactions. 

I wish to apply corrections for a dilute bimolecular reaction, 0.1 mol dm-3 at 25 degC (298K) in water. Are there any simple correction factors that can be applied to diffusion, viscosity, ionic strength and/or solvent dielectric properties. Any help would be appreciated. If the messages tell me its complicated I will simply relent. 

James Robinson
Molecular Modeller
Pharmacy Dept.
Bath University
Bath, UK.
 






From chemistry-request@ccl.net Mon Jun 21 14:32:37 2004
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From: caroline taylor <cmtaylor*at*kff1.uchicago.edu>
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Hello, all.

I'm trying to get version 8 of the intel fortran compiler working (ifc7
is fine), and everything runs fine if I do a static build of some
program. The compiler appears to build/install correctly, and will build a
(dynamic) executable, but I get the following error when I try to run that
executable:

./a.out: error while loading shared libraries: libcxa.so.5: cannot open
shared object file: No such file or directory


The file _is_ in the directory that the compiler looks in:
> ls -l /opt/intel_fc_80/lib/ 
-rw-r--r--    1 root     root       229564 Oct 29  2003 libcxa.a
-rw-r--r--    1 root     root         1052 Oct 29  2003 libcxaguard.a
-rwxr-xr-x    1 root     root           27 Oct 29  2003 libcxaguard.so
-rwxr-xr-x    1 root     root         2496 Oct 29  2003 libcxaguard.so.5
-rwxr-xr-x    1 root     root           22 Oct 29  2003 libcxa.so
-rwxr-xr-x    1 root     root       172615 Oct 29  2003 libcxa.so.5

and the $LD_LIBRARY_PATH variable is set correctly in the run scripts
(this is the only suggestion provided by Intel, and hasn't helped anyone
else, either).

Does anyone out there have a solution to this?

Thanks in advance!!!
	Caroline

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Dr. Caroline M. Taylor
Department of Chemistry
University of Chicago, James Franck Institute
5640 S. Ellis Avenue
Chicago, Illinois 60637
(773) 702-7223
http://kff1.uchicago.edu/~cmtaylor
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