From owner-chemistry@ccl.net Wed Jun 17 04:07:00 2009
From: "Mi yang agri_chemist.:.yahoo.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: HOMO_LUMO gap and Transition Energies
Message-Id: <-39536-090617031959-1386-r8LTHNWz8Xpd1vUHsYy0Fw{=}server.ccl.net>
X-Original-From: "Mi  yang" <agri_chemist*o*yahoo.com>
Date: Wed, 17 Jun 2009 03:19:56 -0400


Sent to CCL by: "Mi  yang" [agri_chemist|*|yahoo.com]
Dear CCL users,
I want to discuss a confusion about Molecular orbital energies. I have optimized an open shell system at MP2\6-31+G* level of theory. Then run its single point CIS calculations to compute it transition energies. My crucial low energy transitions let say have values of 1.5 eV, 2.5 eV and 3.5 eV for H-L, H-L+1 and H-L+2. But when I look the H-Ls energy gaps that are very large than these transitions energies i.e. 5.2 eV, 6.1 eV etc.

Now I am wondering what kind of relation exits in my case between H-L energy gap and electron transitions form these orbitals.

Is it possible that transition energy for H-L can be different form the energy gap of H-L orbitals? Any comment or ref would be highly appreciative. 

Thanks

Miyang

agri_chemist++yahoo.com


From owner-chemistry@ccl.net Wed Jun 17 13:12:01 2009
From: "Anastasios George Papadopoulos anastp---chem.auth.gr" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: ADF-NICS
Message-Id: <-39537-090617102134-15193-WAblihHHRp0J61iRYD+s6w\a/server.ccl.net>
X-Original-From: "Anastasios George Papadopoulos" <anastp : chem.auth.gr>
Date: Wed, 17 Jun 2009 10:21:30 -0400


Sent to CCL by: "Anastasios George Papadopoulos" [anastp!A!chem.auth.gr]
Hello CCL'S Subscribers,

I want to run a NICS calculation, using ADF Package. I manage to do it, but I have one more question. How I could appear the table, which include the "GAUGE INVARIANCE" of every orbital contribution in paramagneting shielding? Like the tables of occupied-occupied and occupied-vertical orbitals contribution in paramagneting shielding.

Thanks in advance, 

Papadopoulos G. Anastasios


From owner-chemistry@ccl.net Wed Jun 17 14:19:01 2009
From: "Jim Kress ccl_nospam__kressworks.com" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL: Question about GAMESS/TINKER - no link atoms
Message-Id: <-39538-090616171829-3811-LlVmcsOIAH5Q0wDNKujL+Q[#]server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam]^[kressworks.com>
Content-Transfer-Encoding: 7bit
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	charset="us-ascii"
Date: Tue, 16 Jun 2009 17:02:31 -0400
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Sent to CCL by: "Jim Kress" [ccl_nospam^^kressworks.com]
It appears you are hosed, at least with this version of GAMESS.  Try
FireFly:

http://classic.chem.msu.su/gran/gamess/index.html

I know it does not require a linkage between the QM and MM subunits.

Jim 

> -----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com^^ccl.net 
> [mailto:owner-chemistry+ccl_nospam==kressworks.com^^ccl.net] 
> On Behalf Of Shahar Keinan skeinan],[gmail.com
> Sent: Tuesday, June 16, 2009 2:44 PM
> To: Kress, Jim 
> Subject: CCL: Question about GAMESS/TINKER - no link atoms
> 
> Dear Jim,
> 
> I did try this, and got the following error message:
> ....
> Parameter file unit number    1
>       *** TINKER INTIALIZATION COMPLETE ***
>  
>  ---- QMMM procedure is ON ----
> 
>           LINKING ATOM PAIRS
>           ------------------
>            NO    QM-ATOM    MM-ATOM
>                *** ERROR IN LINK SPECIFICATION *** 
>                 QMMM REQUIRES at least one Linkge ....
> 
> 
> Best,
> Shahar
> 
> 
> 
> On Tue, Jun 16, 2009 at 8:42 AM, Jim Kress 
> ccl_nospam,kressworks.com <owner-chemistry^-^ccl.net> wrote:
> 
> 
> 
> 	Sent to CCL by: "Jim Kress" [ccl_nospam---kressworks.com]
> 	Did you try to run it or is this a purely hypothetical question?
> 	
> 	I'd suggest you try to run your test case and see what happens.
> 	
> 	Jim
> 	
> 	> -----Original Message-----
> 	> From: owner-chemistry+ccl_nospam==kressworks.com+*+ccl.net
> 	> [mailto:owner-chemistry+ccl_nospam 
> <mailto:owner-chemistry%2Bccl_nospam> ==kressworks.com+*+ccl.net]
> 	> On Behalf Of Shahar Keinan skeinan*_*gmail.com
> 	> Sent: Monday, June 15, 2009 10:51 AM
> 	> To: Kress, Jim
> 	> Subject: CCL: Question about GAMESS/TINKER - no link atoms
> 	>
> 	>
> 	> Sent to CCL by: "Shahar  Keinan" [skeinan^gmail.com] Dear all,
> 	>
> 	> I have submitted this question about a week ago, and have not
> 	> heard anything back. I have also submitted this question to
> 	> the GAMESS forum, with no reply. I am trying again.
> 	>
> 	> I am trying to do a QM/MM calculation with GAMESS/TINKER,
> 	> however, I want to run the calculations without link atoms.
> 	> Is this possible?
> 	> The example files all have link atoms in them.
> 	>
> 	> Thank you,
> 	> Dr. Shahar Keinan
> 	> Duke University
> 	>
> 	>
> 	> I am attaching an example of an input file that gets an error
> 	> message (this is  a water dimer, one water molecule QM, the
> 	> other TIP3):
> 	>
> 	> !  An example file to perform
> 	> !  QM/MM.
> 	> !  water dimer, no link atoms. One water is TIP3, !  other
> 	> water described with HF/STO-3G !
> 	>  $CONTRL SCFTYP=RHF RUNTYP=optimize COORD=UNIQUE NZVAR=33
> 	> $END  $BASIS  GBASIS=sto NGAUSS=3  $END
> 	>  $ZMAT   DLC=.T. AUTO=.T. $END
> 	>  $DATA
> 	> Ab initio atoms in QM region
> 	> C1
> 	> O           8.0  -0.032947       0.000000       0.005966
> 	> H           1.0   0.270601       0.000000       0.911928
> 	> H           1.0   0.792970       0.000000      -0.510216
> 	>  $END
> 	>  $LINK IMOMM=.T. IQMATM(1)=1,2,3 $END
> 	>  $TINKEY
> 	> parameters /home/skeinan/gamess_tinker/tinker/params/charmm
> 	>  $END
> 	>  $TINXYZ
> 	> 6  water dimer
> 	> 1  OT  -0.032947    0.000000    0.005966  91     2     3
> 	> 2  HT   0.270601    0.000000    0.911928  83     1
> 	> 3  HT   0.792970    0.000000   -0.510216  83     1
> 	> 4  HT   2.756636    0.756897   -1.740089  83     5
> 	> 5  OT   2.373120    0.000000   -1.290448  91     4     6
> 	> 6  HT   2.756636   -0.756897   -1.740089  83     5
> 	>  $END
> 	>
> 	>
> 	>
> 	> -= This is automatically added to each message by the mailing
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> 	> message, please change the strange characters on the top line
> 	> to the +*+ sign. You can also look up the 
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> 	> in the mail header.> Conferences:
> 	> http://server.ccl.net/chemistry/announcements/conferences/>
> 	>
> 	
> 	
> 	
> 	-= This is automatically added to each message by the 
> mailing script =-
> 	
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> 	
> 	E-mail to subscribers: CHEMISTRY^-^ccl.net or use:> 	
> 	E-mail to administrators: CHEMISTRY-REQUEST^-^ccl.net or use> 	Conferences: 
> http://server.ccl.net/chemistry/announcements/conferences/
> 	
> 	Search Messages: 
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>


From owner-chemistry@ccl.net Wed Jun 17 14:54:01 2009
From: "Mark Zottola mzottola . gmail.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: Singlet to Multiplet PE Surfaces
Message-Id: <-39539-090617140947-27405-fiEbAZGe9n//KFifYUHeUg!^!server.ccl.net>
X-Original-From: Mark Zottola <mzottola+*+gmail.com>
Content-Type: multipart/alternative; boundary=0016364d1dc5b16b8a046c8e8a1e
Date: Wed, 17 Jun 2009 13:22:54 -0400
MIME-Version: 1.0


Sent to CCL by: Mark Zottola [mzottola^gmail.com]
--0016364d1dc5b16b8a046c8e8a1e
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I need the more robust theoreticians on this list to settle a debate in my
lab.

I have a system which is in a singlet spin state.  A colleague wants to
calculate the transition state for the oxidation of this system by an oxygen
atom.

I have said I do not believe we can do this as bringing 2 molecular species
in the triplet and singlet states would make location of the transition
state impossible.  The question of multiplicity changeing as the distance
between the two species changing is not something quantum mechanics can do.
My colleague claims his old group did that type of calculation on a very
frequent basis.

So my questions are - am I wrong in thinking that the problem, as posed, is
intractable?  Can you actually quench a spin state in the transition state?
If there are methods to handle this, would anyone be willing to point me to
them?

Thanks!


Mark

--0016364d1dc5b16b8a046c8e8a1e
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<div>I need the more robust theoreticians on this list to settle a debate i=
n my lab.</div>
<div>=A0</div>
<div>I have a system which is in a singlet spin state.=A0 A colleague wants=
 to calculate the transition state for the oxidation of this system by=A0an=
 oxygen atom.</div>
<div>=A0</div>
<div>I have said I do not believe we can do this as bringing 2 molecular sp=
ecies in the triplet and singlet states would make location of the transiti=
on state impossible.=A0 The question of multiplicity changeing as the dista=
nce between the two species changing is not something quantum mechanics can=
 do.=A0 My colleague claims his old group did that type of calculation on a=
 very frequent basis.</div>

<div>=A0</div>
<div>So my questions are - am I wrong in thinking that the problem, as pose=
d, is intractable?=A0 Can you actually quench a spin state in the transitio=
n state?=A0 If there are methods to handle this, would anyone be willing to=
 point me to them?</div>

<div>=A0</div>
<div>Thanks!</div>
<div>=A0</div>
<div>=A0</div>
<div>Mark</div>

--0016364d1dc5b16b8a046c8e8a1e--


From owner-chemistry@ccl.net Wed Jun 17 15:50:01 2009
From: "Cihan Aydin cihan.aydin~!~umassmed.edu" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: PCA and distance-covariance questions...
Message-Id: <-39540-090617014838-26720-wEW770naM9eXKv/+v00s3g|server.ccl.net>
X-Original-From: "Cihan Aydin" <cihan.aydin::umassmed.edu>
Content-Type: multipart/mixed;
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Date: Tue, 16 Jun 2009 21:48:18 -0400
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Sent to CCL by: "Cihan Aydin" [cihan.aydin,,umassmed.edu]

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I am sorry but I forgot to put the subject in my first e-mail so I am
reposting it.

Thank you

-- 
Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student -$- Schiffer Lab

364 Plantation St. LRB 970M
Worcester, MA 01605

cihan.aydin-$-umassmed.edu
+1 (508) 856-3430

--=-q3xgKgno7bnEB9zSMr6d
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> From: "Cihan Aydin" <cihan.aydin-$-umassmed.edu>
To: chemistry-$-ccl.net
Message-ID: <1245203202.4126.6.camel-$-Barad-Dur.cable.rcn.com>
MIME-Version: 1.0
X-Mailer: Evolution 2.26.1
Date: Tue, 16 Jun 2009 21:46:43 -0400
Subject: 
Content-Type: text/plain
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Dear CCL community,

I have a couple of questions. 

First of all, in order to nullify the effects of alignment when doing
PCA analysis, I would like to do a distance-covariance analysis on my
trajectories. The principal reference I found was the Abseher and Nilges
(1998) paper called -Is there any non-trivial dynamic cross
correlations?- they go through the methodology and comparison of
different alignments and distance-covariance matrix. One thing they do
is to create "reduced" covariance matrices by linear combination. I
could not really understand the biological and physical relevance of
such a combination. If you know about this, can you direct me to a
suitable resource and/or shed light on this subject? Can we use these
reduced covariance matrices to get essential subspace? How can we
process that information?

Second, what is the advantage of reducing the covariance matrix from
coordinate space to dihedral space? I tried to find appropriate
references to research that did that but could not come with any.

Third, I have read some papers that argued strongly against the validity
of PCA analysis. The principal concern was that the sampling time
usually used (the most I have seen was 3ns) was not enough to achieve
convergence (a nice paper was from Rueda et al. - they used 100ns
simulations like 30 proteins and argued against the reproducibility of
MD trajectories from only a slice of the timeframe). If you had any
personal experience with PCA, what is your opinion about this?


Thank you for your time.

-- 
Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student -$- Schiffer Lab

364 Plantation St. LRB 970M
Worcester, MA 01605

cihan.aydin-$-umassmed.edu
+1 (508) 856-3430

--=-q3xgKgno7bnEB9zSMr6d--


From owner-chemistry@ccl.net Wed Jun 17 16:58:00 2009
From: "Jim Kress ccl_nospam[-]kressworks.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Singlet to Multiplet PE Surfaces
Message-Id: <-39541-090617164257-20936-hG58VXazQpuDwbExVCaUvw() server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam[#]kressworks.com>
Content-Transfer-Encoding: 7bit
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	charset="us-ascii"
Date: Wed, 17 Jun 2009 16:31:19 -0400
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Sent to CCL by: "Jim Kress" [ccl_nospam * kressworks.com]
So basically you want to do this reaction (A is your molecule):

 A(singlet) + O(triplet)  => A-O

An example of this would be

H2(singlet) + O(triplet)  => H2O 

Which is certainly calcuable and happeneds in nature on a continuous basis.
It may or may not have a transition state in the gas phase but I'm sure you
could find examples of oxidation reactions that do.

Jim

> -----Original Message-----
> From: owner-chemistry+ccl_nospam==kressworks.com%x%ccl.net 
> [mailto:owner-chemistry+ccl_nospam==kressworks.com%x%ccl.net] 
> On Behalf Of Mark Zottola mzottola . gmail.com
> Sent: Wednesday, June 17, 2009 1:23 PM
> To: Kress, Jim 
> Subject: CCL: Singlet to Multiplet PE Surfaces
> 
> I need the more robust theoreticians on this list to settle a 
> debate in my lab.
>  
> I have a system which is in a singlet spin state.  A 
> colleague wants to calculate the transition state for the 
> oxidation of this system by an oxygen atom.
>  
> I have said I do not believe we can do this as bringing 2 
> molecular species in the triplet and singlet states would 
> make location of the transition state impossible.  The 
> question of multiplicity changeing as the distance between 
> the two species changing is not something quantum mechanics 
> can do.  My colleague claims his old group did that type of 
> calculation on a very frequent basis.
>  
> So my questions are - am I wrong in thinking that the 
> problem, as posed, is intractable?  Can you actually quench a 
> spin state in the transition state?  If there are methods to 
> handle this, would anyone be willing to point me to them?
>  
> Thanks!
>  
>  
> Mark
>


From owner-chemistry@ccl.net Wed Jun 17 17:45:01 2009
From: "Nuno A. G. Bandeira nuno.bandeira++ist.utl.pt" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: ADF-NICS
Message-Id: <-39542-090617174358-17956-61ExEcgEI6Yy2M6+alOZKA~~server.ccl.net>
X-Original-From: "Nuno A. G. Bandeira" <nuno.bandeira]_[ist.utl.pt>
Content-Transfer-Encoding: 7bit
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Date: Wed, 17 Jun 2009 22:43:38 +0100
MIME-Version: 1.0


Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira]=[ist.utl.pt]
Anastasios George Papadopoulos anastp---chem.auth.gr wrote:
> Sent to CCL by: "Anastasios George Papadopoulos" [anastp!A!chem.auth.gr]
> Hello CCL'S Subscribers,
> 
> I want to run a NICS calculation, using ADF Package. I manage to do it, but I have one more question. How I could appear the table, which include the "GAUGE INVARIANCE" of every orbital contribution in paramagneting shielding? Like the tables of occupied-occupied and occupied-vertical orbitals contribution in paramagneting shielding.

Dear Anastasios,

Try the following block keys in EPR:

$ADFBIN/epr <<EOR

CLGEPR
  OUTPUT
   SIZE BIGDEBUG
   CRITERIA 0.0000001
   SumUpOccVir
   Format D
   PrintMat
  SUBEND
END

END INPUT

It will produce a very big output but I think you will get what you need.

Cheers,
Nuno


-- 
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student - - IST,Lisbon
--


From owner-chemistry@ccl.net Wed Jun 17 18:20:01 2009
From: "David Gallagher gallagher.da{=}gmail.com" <owner-chemistry-.-server.ccl.net>
To: CCL
Subject: CCL: COSMOtherm on Macintosh
Message-Id: <-39543-090617172657-8082-Sb7aPnax/jRoiP7aTAhYgg-.-server.ccl.net>
X-Original-From: David Gallagher <gallagher.da|*|gmail.com>
Content-Type: multipart/alternative;
	boundary="=====================_20991156==.ALT"
Date: Wed, 17 Jun 2009 14:20:10 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da**gmail.com]
--=====================_20991156==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

The COSMOtherm package for prediction of thermodynamic properties, is 
now available for the Macintosh platform, in addition to Windows and 
Linux.  For more information or to request a demo version, visit 
<http://cacheresearch.com/cosmo.html>http://cacheresearch.com/cosmo.html

COSMOtherm is used for predicting properties in mixtures and ionic 
liquids including: vapor pressures, solubilities, ADME properties, 
partition coefficients, phase equilibria, phase diagrams, azeotropes, 
heat of mixing, reaction thermodynamics, activity coefficients, sigma 
profiles, pKa and much more.   It is widely used in chemical process 
engineering, environmental chemistry, and life sciences.  The 
award-winning COSMOtherm's underlying methodology is based on quantum 
chemistry and statistical thermodynamics.  An extensive bibliography 
can be found at 
<http://www.cacheresearch.com/cosmobibindex.html>http://www.cacheresearch.com/cosmobibindex.html 
.

To find out more, please contact 
<http://www.cosmologic.de/index.php?cosId=1200&crId=1>COSMOlogic in 
Europe, or <http://cacheresearch.com/>CAChe Research in North and 
South America.

--=====================_20991156==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
The COSMOtherm package for prediction of thermodynamic properties, is now
available for the Macintosh platform, in addition to Windows and
Linux.&nbsp; For more information or to request a demo version, visit
<a href="http://cacheresearch.com/cosmo.html">
http://cacheresearch.com/cosmo.html</a> <br><br>
COSMOtherm is used for predicting properties in mixtures and ionic
liquids including: vapor pressures, solubilities, ADME properties,
partition coefficients, phase equilibria, phase diagrams, azeotropes,
heat of mixing, reaction thermodynamics, activity coefficients, sigma
profiles, pKa and much more.&nbsp;&nbsp; It is widely used in chemical
process engineering, environmental chemistry, and life sciences.&nbsp;
The award-winning COSMOtherm's underlying methodology is based on quantum
chemistry and statistical thermodynamics.&nbsp; An extensive bibliography
can be found at
<a href="http://www.cacheresearch.com/cosmobibindex.html">
http://www.cacheresearch.com/cosmobibindex.html</a>&nbsp; .&nbsp;
<br><br>
To find out more, please contact
<a href="http://www.cosmologic.de/index.php?cosId=1200&amp;crId=1">
COSMOlogic</a> in Europe, or <a href="http://cacheresearch.com/">CAChe
Research</a> in North and South America.<br>
</body>
</html>

--=====================_20991156==.ALT--