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Subject: Re: CCL:Hi, do anyone know how to solvate a sngle proton in G03?
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Well, maybe the calculations are possible from technical point of view.
But are you sure that free H(+) ion can exist in the water environment??
It is obvious that the hydronium ion must be formed.
Maybe Gaussian is an example of artificial intelligence computer code and
it does not want to performed such calculations

Kzys

> Hi, everyone,
> my input:
> #p... scrf(iefpcm,H2O)...
>
> 1 1
> H .0 .0 .0
>
> radii=bondi
> ----------------------------------------------
> But it doesn't work
>
> err message:
> United  Atom Topological Model (UAO parameters set).
>  UA0: Hydrogen    1 is unbound. Keep it explicit at all point on the
> UA0: potential energy surface to get meaningful results.
> ----------------------------------------------
> Is such a calculation possible?
> In fact, I want to find the free energy of H(+) in water, is it assumed
> as 0?
>
> Thanks
>
> Jing Song
>
>
>
> -= This is automatically added to each message by the mailing script =-
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Krzysztof Zborowski
Faculty of Chemistry
Jagiellonian University
3 Ingardena Street
30-060 Krakow
Poland
phone: +48(12)632-4888 ext. 2064 or 2067
fax:  +48(12)634-05-15
email: zborowsk[at]chemia.uj.edu.pl
ICQ 158385743
gg 3817259




From chemistry-request@ccl.net Fri Apr 22 04:25:19 2005
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From: Matthias Mann <Matthias.Mann[at]chemie.tu-dresden.de>
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Subject: Re: CCL:Arguslab is also free docking software for teaching and academic research :)
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Aah, Version 4.1 ?  Where can I find this?
More stable than Ver. 4.0.1 ?

BTW, the releases after 4.0beta does no longer run without administrator
rights under Windows, so the use is problematic for teaching in computer
pools ...

Greetings,
Matthias

On Thursday 21 April 2005 18:35, you wrote:
> I could not resist :)
>
> ArgusLab 4.1 is completely free for everyone and has a terrific docking
> suite.  The ShapeDock engine in ArgusLab is an "exhaustive" search
> algorithm of my own invention and is very fast.
>
> ArgusLab also includes a large suite of electronic structure capabilities
> including EHT, AM1, PM3, ZINDO, and a terrific interface to Gaussian 98 and
> Gaussian 03.  Also included is a nice 3D molecule builder and extensive
> support for visualizing  results, surfaces, etc.
>
> Get it for free at http://www.arguslab.com
>
> Cheers,
> Mark

-- 
Dr. Matthias Mann 
DV-Koordinator Fachrichtung Chemie und Lebensmittelchemie
TU Dresden, D-01062 Dresden, Tel./Fax: +49 (351) 463-34286
Email: Matthias.Mann~at~chemie.tu-dresden.de


From chemistry-request@ccl.net Fri Apr 22 05:30:16 2005
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Subject: Summary: Effect of oxidation on electron density
From: "Noel O'Boyle" <noel.oboyle2{at}mail.dcu.ie>
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Thanks to everyone who replied to my original question about the
similarity between the change in electron density after oxidation, and
spin density of the resulting oxidised species:
David Close, James Kirkpatrick, Cory Pye, James Eilers and Mikael
Johansson.

The answers are given below.

Regards,
Noel O'Boyle.
--------------------

Original question:
--------------------
Dear CCLers,

I have a question related to visualising the instantaneous change in
electron density accompanying oxidation (of a metal complex).

I am using Gaussian03 and have calculated the electron density of the
molecule in its oxidised state (at the geometry of the native state) and
subtracted this from the electron density of the molecule in its native
state. 

However, I have just noticed that the total spin density of the oxidised
molecule gives an almost identical picture. Is this true in general? (I
don't have a good understanding of what the total spin density shows.)

Regards,
Noel O'Boyle,
University College Dublin.
--------------------

Answers:

David Close:
--------------------
I am not sure I understand the question.  But it may have to do with
electron density versus spin density.  Since you are removing an
electron, you are creating a radical.  True spin densities are defined
as the difference between alpha and beta spin densities.  You can see
this two ways.  The easiest is at the end of the printout where the Sum
of the Mulliken spin densities are printed.  So just looking at the
Isotropic hyperfine couplings tells you which atoms have significant
hyperfine couplings.  To see where these came from you have to do a
population analysis, and at the very end you will get a Gross orbital
population where you can find the difference in alpha and beta spins. 
--------------------

James Kirkpatrick:
--------------------
this is my(probably poor)  understanding of the problem!

The total spin density for the neutral molecule will be 0 everywhere 
because the wave function is "restricted", i.e. wherever there is an 
"up" electron there is also a "down" electron.

For the oxidised molecules, if you use an unrestricted wavefunction the 
spin density will be more or less the spatial distribtuion of 
probability of finding  an unpaired electron (most electrons will be 
more or less paired up in corresponding alpha and beta MOs, so will 
produce no net spin density, but the unpaired alpha HOMO will be 
unpaired), which will be very similar (identical if you use a retricted 
open shell slater determinant?) to the difference in charges betwee the 
neutral and charged molecules.

Does that explain it more or less? Let me know if you get interesting 
answers to this interesting question!
--------------------

James Eilers:
--------------------
If you are doing RHF, yes.
Total spin density is the excess of "alpha electron density" over "beta 
electron density".
So if you remove 1 electron (oxidation) from the HOMO of  a ground  
state singlet  wavefunction and that HOMO  orbital is
fairly similar in the resulting cation (doublet), the density  
difference and the spin density will look very much alike.
--------------------

Cory Pye:
--------------------
Let
alpha = electron density of spin-up electrons
beta  = electron density of spin-down electrons.
alpha+beta = total electron density
alpha-beta = spin density

We will assume a 2N electron system (convention) from which we remove an
alpha
electron.
let a superscript 0,+ denote the native and oxidized species
let a subscript N indicate the number of electrons.

You have calculated
J=(alpha^+_N-1 + beta^+_N) - (alpha^0_N + beta^0_N) .

The spin density is
alpha^+_N-1 - beta^+_N

Note that

J=(alpha^+_N-1 - beta^+_N) + (beta^+_N - alpha^0_N) + (beta^+_N -
beta^0_N)

If the removal of the alpha electron doesn't affect muct the electrons
of
opposite spin, then the final term disappears because
beta^+_N = beta^0_N

The middle term simplifies to beta^0_N - alpha^0_N. If the native
species is
closed-shell, then it has no spin density and the middle term is 0.

Under these conditions, the spin density of the reduced species remains.

J = alpha^+_N-1 - beta^+_N
--------------------

Mikael Johansson:
--------------------
No. Spin density and total electron density difference are two different
and more or less independent creatures, though they _can_ be located to 
similar regions of the molecule (as apparently for you). Spin density is
much more free to change after, for example, oxidation/reduction. The 
electron density is much more restricted as it is bound by classical 
electrostatic forces.

I've done some studies comparing electron and spin density changes
during 
oxidation/reduction of iron porphyrins [1-3]. Perhaps they are of some 
interest.

[1] M.P. Johansson, M.R.A. Blomberg, D. Sundholm, M. WikstrC6m, "Change
in
     electron and spin density upon electron transfer to haem", Biochim.
     Biophys. Acta - Bioenergetics 1553 (2002) 183-187.
[2] M.P. Johansson, D. Sundholm, G. Gerfen, M. WikstrC6m, "The Spin
     Distribution in Low-Spin Iron Porphyrins", J. Am. Chem. Soc. 124
     (2002) 11771-11780
[3] M.P. Johansson, D. Sundholm, "Spin and charge distribution in iron
     porphyrin models: A coupled cluster and density-functional study",
     J. Chem. Phys. 120 (2004) 3229-3236.
--------------------



From chemistry-request@ccl.net Fri Apr 22 03:23:17 2005
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Subject: Re: CCL:More on Compiling g03 on Opteron with pgf 5.2-4
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On Thu, 21 Apr 2005, Christian Boehme wrote:

> I have tried to compile Gaussian03 on our Opteron machines running under
> SuSE SLES 9 using pgf version 5.2-4. While PGI 5.2-x is the supported
> compiler suite according to gaussian.com webpages the build scripts of
> our g03 version still contain 5.1 pathnames. I fixed this and Gaussian
> seemed to compile without errors. However, the resulting binaries
> segfault after just a few lines of output:
>
>  Entering Gaussian System, Link 0=g03
>  Initial command:
>  /usr/product/gaussian64/g03/l1.exe
> /home/gwdg/GWDG/cboehme1/test/g03tests/Gau-28741.inp -scrdir=/ho
> me/gwdg/GWDG/cboehme1/test/g03tests/
>
> I looked at the strace and seemingly l1.exe segfaults for no obvious
> reasons.

Hi,
What kernel are you running? My executables produced the same segfault 
using a 2.4.x kernel, but were running perfectly with 2.6.11.

cheers,
dino




From chemistry-request@ccl.net Fri Apr 22 09:56:29 2005
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 22 Apr 2005 14:56:12 +0200 (MET-DST)
Date: Fri, 22 Apr 2005 14:56:12 +0200 (MET-DST)
From: forli <> unisi.it
Subject: RE: CCL:Molecule coordinates to  .3ds, .dxf  or  .cad files
To: h.rzepa <> imperial.ac.uk
Cc: chemistry <> ccl.net
Message-id: <01LNECYIORSY91W3U5 <> mailsrv.unisi.it>
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There are different ways to make conversion.
You can do a PDB->VRML conversion using RasMol or other softwares, and
then VRML->3ds/dxf.
Depending on what chemical tool you use make first conversion, you can
get ribbons, cartoons, CPK and so on...
Second step will be the most difficult, I think, because at my knowledge
there are no free tools to do that.

Here you can find few links:
http://www.pc.chemie.tu-darmstadt.de/research/vrml/pdb2vrml_right.shtml
http://www.sienahts.edu/~che/vrmlchem.html

http://www.okino.com/conv/imp_pdb.htm Shareware tool to convert directly
PDB->3ds/dxf (some limiatations)

If you find some free stuff to do everithing, please let me know.

ciao,

Stefano



p.s. ...and you can post some snapshots of final product :)


---

***********************************
 Stefano Forli
 Dip. Farmaco Chimico Tecnologico  
 Universita' degli Studi di Siena  
 Via Aldo Moro                    
 I-53100 Siena, Italy              
 Phone: ++39 0577 234307      
 Fax: ++39 0577 234333   
 e-mail: forli <> unisi.it
***********************************


From chemistry-request@ccl.net Fri Apr 22 17:08:03 2005
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Subject: RE: Hi, do anyone know how to solvate a sngle proton in G03?
Date: Fri, 22 Apr 2005 15:08:23 -0400
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Thread-Topic: Hi, do anyone know how to solvate a sngle proton in G03?
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From: "Shobe, David" <dshobe * sud-chemieinc.com>
To: <zborowsk * chemia.uj.edu.pl>, <chemistry * ccl.net>
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If I remember correctly the cavity (which contains the molecule and from which the solvent is excluded) for the SCRF calculation is derived from the electron density.  That could be a problem with H+.  :-)

You might get a usable solvation energy for "H+(aq)" by calculating SCRF for H3O+ and H2O, then subtracting the energies.  The idea is that the equation:
	 H+(aq) + H2O(aq) == H3O+(aq)
ought to be thermoneutral.

--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 * ccl.net] On Behalf Of zborowsk * chemia.uj.edu.pl
Sent: Friday, April 22, 2005 8:04 AM
To: sjsongjing * gmail.com
Cc: chemistry * ccl.net
Subject: CCL:Hi, do anyone know how to solvate a sngle proton in G03?

Well, maybe the calculations are possible from technical point of view.
But are you sure that free H(+) ion can exist in the water environment??
It is obvious that the hydronium ion must be formed.
Maybe Gaussian is an example of artificial intelligence computer code and it does not want to performed such calculations

Kzys

> Hi, everyone,
> my input:
> #p... scrf(iefpcm,H2O)...
>
> 1 1
> H .0 .0 .0
>
> radii=bondi
> ----------------------------------------------
> But it doesn't work
>
> err message:
> United  Atom Topological Model (UAO parameters set).
>  UA0: Hydrogen    1 is unbound. Keep it explicit at all point on the
> UA0: potential energy surface to get meaningful results.
> ----------------------------------------------
> Is such a calculation possible?
> In fact, I want to find the free energy of H(+) in water, is it 
> assumed as 0?
>
> Thanks
>
> Jing Song
>
>
>
> To send e-mail to subscribers of CCL put the string CCL: on your
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST * ccl.net  HOME Page: http://www.ccl.net   | Jobs Page:
> http://www.ccl.net/jobs
>
> use the Web based form from CCL Home Page


Krzysztof Zborowski
Faculty of Chemistry
Jagiellonian University
3 Ingardena Street
30-060 Krakow
Poland
phone: +48(12)632-4888 ext. 2064 or 2067
fax:  +48(12)634-05-15
email: zborowsk * chemia.uj.edu.pl
ICQ 158385743
gg 3817259




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From chemistry-request@ccl.net Fri Apr 22 12:43:53 2005
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To: "Matthias Mann" <Matthias.Mann <> chemie.tu-dresden.de>, <chemistry <> ccl.net>
Subject: RE: Arguslab is also free docking software for teaching and academic research :)
Date: Fri, 22 Apr 2005 09:43:42 -0700
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Hi Matthias,

Oops, I was so excited I transposed a couple of digits....
4.01 is the latest version.

I'll look into the administrator rights issue.

Cheers,
Mark

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request <> ccl.net]On
Behalf Of Matthias Mann
Sent: Friday, April 22, 2005 12:21 AM
To: chemistry <> ccl.net
Subject: CCL:Arguslab is also free docking software for teaching and
academic research :)



Aah, Version 4.1 ?  Where can I find this?
More stable than Ver. 4.0.1 ?

BTW, the releases after 4.0beta does no longer run without administrator
rights under Windows, so the use is problematic for teaching in computer
pools ...

Greetings,
Matthias

On Thursday 21 April 2005 18:35, you wrote:
> I could not resist :)
>
> ArgusLab 4.1 is completely free for everyone and has a terrific docking
> suite.  The ShapeDock engine in ArgusLab is an "exhaustive" search
> algorithm of my own invention and is very fast.
>
> ArgusLab also includes a large suite of electronic structure capabilities
> including EHT, AM1, PM3, ZINDO, and a terrific interface to Gaussian 98
and
> Gaussian 03.  Also included is a nice 3D molecule builder and extensive
> support for visualizing  results, surfaces, etc.
>
> Get it for free at http://www.arguslab.com
>
> Cheers,
> Mark

--
Dr. Matthias Mann
DV-Koordinator Fachrichtung Chemie und Lebensmittelchemie
TU Dresden, D-01062 Dresden, Tel./Fax: +49 (351) 463-34286
Email: Matthias.Mann <> chemie.tu-dresden.de


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