From owner-chemistry@ccl.net Wed Aug 18 02:40:00 2010 From: "Robert McGibbon rmcgibbo{=}princeton.edu" To: CCL Subject: CCL: bader chargers Message-Id: <-42549-100818023349-15732-gKt+0WZk73VhCp15rPCSNw_._server.ccl.net> X-Original-From: Robert McGibbon Content-Type: multipart/alternative; boundary=0016363b8b88236485048e133fad Date: Wed, 18 Aug 2010 02:33:41 -0400 MIME-Version: 1.0 Sent to CCL by: Robert McGibbon [rmcgibbo||princeton.edu] --0016363b8b88236485048e133fad Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Seems very simple. They just subtract the number of electrons in the Bader region from the number of protons. Thus, the partial charge on oxygen is 8 - 9.1566 =3D -1.157, and in the hydrogen region it's 1 - 0.4238 =3D +0.576. Here's the relevant section of the paper: =3D=3D=3D=3D Three Bader regions were found, each containing one atom. The total charge in each one of the regions around the hydrogen atoms contained 0.4238 electrons and the oxygen region contained 9.1566 electrons, which gives a sum of 10.0041 electrons. The atomic partial charges are the same as found by Bader [2](se= e Table 1), showing that these two different algorithms yield the same results. ------------------------------ Table 1. Partial charge of oxygen and hydrogen in an isolated water molecule Partial charge ------------------------------ O atomH atoms Bader's original work-1.16+0.58 This work-1.157+0.576 ---- Robert McGibbon Princeton University Undergraduate Class of 2011 On Tue, Aug 17, 2010 at 11:32 PM, neranjan perera neranjan007]*[gmail.com < owner-chemistry]^[ccl.net> wrote: > Hi, > In the paper " G. Henkelman et al. / Computational Materials Science 36 > (2006) 354-360" , they have got bader chargers for water (H2O) as, > For Hydrogen 0.4238 e > Oxygen 9.1566 e > > and then converted these Bader chargers into atomic partial charges; > Hydrogen +0.58 > Oxygen -1.16 > > So I want to know how to do the above conversion ? > > > Thanks > Neranjan Perera. > > > > > On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kaminski rkaminski.rk[#] > gmail.com > wrote: > >> What do you understand by these 'atomic partial charges'? >> >> Radek >> >> >> 2010/8/17 neranjan perera neranjan007!A!gmail.com < >> owner-chemistry|,|ccl.net > >> >> Hi, >>> how can i convert "bader chargers" to "atomic partial chargers"? >>> >>> Thanks. >>> >>> >>> Neranjan Perera. >>> neranjan007 *-* gmail.com >>> >>> -- >>> Graduate Student >>> Department of Chemistry >>> University of Connecticut >>> >>> >>> >> >> >> -- >> Radoslaw Kaminski, M.Sc. Eng. >> Ph.D. Student >> Crystallochemistry Laboratory >> Department of Chemistry >> University of Warsaw >> Pasteura 1, 02-093 Warszawa, Poland >> http://acid.ch.pw.edu.pl/~rkaminski/ > > --0016363b8b88236485048e133fad Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Seems very simple. They just s= ubtract the number of electrons in the Bader region from the number of prot= ons. Thus, the partial charge on oxygen is 8 - 9.1566 =3D -1.157, and = in the hydrogen region it's 1 - 0.4238 =3D +0.576. 

Here's the relevant section of the paper:

<= p>=3D=3D=3D=3D

Three Bader regions were found, each containing one atom. The total charge in each one of the regions around the hydrogen atoms contained 0.4238=20 electrons and the oxygen region contained 9.1566 electrons, which gives a sum of 10.0041 electrons. The atomic partial charges are the same as=20 found by Bader [2] (see Table 1),= showing that these two different algorithms yield the same results.


Table 1.

Partial charge of oxygen and h= ydrogen in an isolated water molecule

Partial charge
O atomH atoms
Bader’s origin= al work−1.16+0.58
This work−1.157+0.576



----
Rober= t McGibbon
Princeton University
Undergraduate Class of 2011

On Tue, Aug 17, 2010 at 11:32 PM, neranjan perera neranjan007]*[gmail.com <owner-chemistry]^[ccl.net> wrote:
Hi,
 In the paper " G. Henkelman et al. / Computational Materi= als Science 36 (2006) 354–360" , they have got bader chargers fo= r water (H2O) as,
For   Hydrogen   0.4238 e
&nb= sp;       Oxygen     9.15= 66 e
 
and then converted these Bader chargers into atomic partial charg= es;
       Hydrogen   +0.58
=        Oxygen      -= 1.16

So I want to know how to do the above conversion ?

Thanks
Neranjan Perera.


            = ;            &n= bsp;            = ;            &n= bsp;            = ;         

On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kaminski rkamins= ki.rk[#]gmail.com <owner-chemistry|ccl.net> wrote:
What do you understand = by these 'atomic partial charges'?

Radek


2010/8/17 neranjan perera neranjan007!A!gmail.com <owner-chemistry|,|ccl.net>

Hi,
   how= can i convert "bader chargers" to "atomic partial chargers&= quot;?

Thanks.


Neranjan Perera.
neranjan007 *-* gmail.com

--
Graduate Student
Department of Chemistry
University of Connecticut




--
Radoslaw Kaminski, M.Sc. Eng.
Ph.D. Student
Cryst= allochemistry Laboratory
Department of Chemistry
University of Warsaw=
Pasteura 1, 02-093 Warszawa, Poland
http:/= /acid.ch.pw.edu.pl/~rkaminski/
--0016363b8b88236485048e133fad-- From owner-chemistry@ccl.net Wed Aug 18 03:26:01 2010 From: "Mohamed Imran PK imranpkm#%#gmail.com" To: CCL Subject: CCL: bader chargers Message-Id: <-42550-100818032138-28933-0+AbhS9wttQ/mlzuVX9k4Q||server.ccl.net> X-Original-From: Mohamed Imran PK Content-Type: multipart/alternative; boundary=001485f27208d82cba048e13e957 Date: Wed, 18 Aug 2010 12:51:25 +0530 MIME-Version: 1.0 Sent to CCL by: Mohamed Imran PK [imranpkm*gmail.com] --001485f27208d82cba048e13e957 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable The numbers have simply been substracted from their atomic numbers, as is done in population analysis schemes PKI On Wed, Aug 18, 2010 at 9:02 AM, neranjan perera neranjan007]*[gmail.com < owner-chemistry- -ccl.net> wrote: > Hi, > In the paper " G. Henkelman et al. / Computational Materials Science 36 > (2006) 354=96360" , they have got bader chargers for water (H2O) as, > For Hydrogen 0.4238 e > Oxygen 9.1566 e > > and then converted these Bader chargers into atomic partial charges; > Hydrogen +0.58 > Oxygen -1.16 > > So I want to know how to do the above conversion ? > > > Thanks > Neranjan Perera. > > > > > On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kaminski rkaminski.rk[#] > gmail.com > wrote: > >> What do you understand by these 'atomic partial charges'? >> >> Radek >> >> >> 2010/8/17 neranjan perera neranjan007!A!gmail.com < >> owner-chemistry|,|ccl.net > >> >> Hi, >>> how can i convert "bader chargers" to "atomic partial chargers"? >>> >>> Thanks. >>> >>> >>> Neranjan Perera. >>> neranjan007 *-* gmail.com >>> >>> -- >>> Graduate Student >>> Department of Chemistry >>> University of Connecticut >>> >>> >>> >> >> >> -- >> Radoslaw Kaminski, M.Sc. Eng. >> Ph.D. Student >> Crystallochemistry Laboratory >> Department of Chemistry >> University of Warsaw >> Pasteura 1, 02-093 Warszawa, Poland >> http://acid.ch.pw.edu.pl/~rkaminski/ >> > > > > -- > > --=20 There are only atoms and space, the rest is opinion. --001485f27208d82cba048e13e957 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable The numbers have simply been substracted from their atomic numbers, as is d= one in population analysis schemes
PKI


On Wed, Aug 18, 2010 at 9:02 AM, neranjan perera neranjan007]*[gmail.com <owner-chemistry- -ccl.net> wrote:
Hi,
=A0In the = paper " G. Henkelman et al. / Computational Materials Science 36 (2006= ) 354=96360" , they have got bader chargers for water (H2O) as,
For=A0=A0 Hydrogen=A0=A0 0.4238 e
=A0=A0=A0=A0=A0=A0=A0 Oxygen=A0=A0=A0= =A0 9.1566 e
=A0
and then converted these Bader chargers into atomic partial charges;=
=A0=A0=A0=A0=A0=A0 Hydrogen=A0=A0 +0.58
=A0=A0=A0=A0=A0=A0 Oxygen= =A0=A0=A0=A0=A0 -1.16

So I want to know how to do the above convers= ion ?


Thanks
Neranjan Perera.


=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0
<= br>
On Tue, Aug 17, 2010 at 9:21 PM, Radoslaw Kam= inski rkaminski.rk[#]gmail.c= om <owner-chemistry|ccl.net> wrote:
What do you under= stand by these 'atomic partial charges'?

Radek


2010/8/17 neranjan perera neranjan007!A!gmail.com <owner-chemistry|,|ccl.net>

Hi,
=A0=A0 how= can i convert "bader chargers" to "atomic partial chargers&= quot;?

Thanks.


Neranjan Perera.
neranjan007 *-* gmail.com

--
Graduate Student
Department of Chemistry
University of Connecticut




--
Radoslaw Kaminski, M.Sc. Eng.
Ph.D. Student
Cryst= allochemistry Laboratory
Department of Chemistry
University of Warsaw=
Pasteura 1, 02-093 Warszawa, Poland
http:/= /acid.ch.pw.edu.pl/~rkaminski/



--




--
There are only atoms an= d space, the rest is opinion.
--001485f27208d82cba048e13e957-- From owner-chemistry@ccl.net Wed Aug 18 07:18:00 2010 From: "abhishekdc(-)iitb.ac.in" To: CCL Subject: CCL:G: about NBO Message-Id: <-42551-100818022717-671-AmL0+hymCLtlUNXMoHsyGA[A]server.ccl.net> X-Original-From: abhishekdc . iitb.ac.in Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=utf-8 Date: Tue, 17 Aug 2010 14:59:57 +0530 MIME-Version: 1.0 Sent to CCL by: abhishekdc]|[iitb.ac.in Dear All, What is the meaning of "NBO donation" and "NBO retrodonation"? What are their interpretation, utility and necessary keywords in G03?? Many thanks in advance. Sincerely, Abhishek From owner-chemistry@ccl.net Wed Aug 18 08:48:01 2010 From: "Sagarika Dev sagarika.dev__gmail.com" To: CCL Subject: CCL:G: NEDA Analysis with NBO keyword in Gaussian03 Message-Id: <-42552-100818073523-11061-L+DqsW5Sb4t/SpanzSKFmg#server.ccl.net> X-Original-From: "Sagarika Dev" Date: Wed, 18 Aug 2010 07:35:20 -0400 Sent to CCL by: "Sagarika Dev" [sagarika.dev%a%gmail.com] Dear All, I was trying to do Natural energy decomposition analysis for a trimer using NBO key word in Gaussian03. I am attaching below the sample input file %chk=gt2_neda.chk %mem=2GB %nprocshared=2 # HF/6-31g(d,p) pop=nboread gt2 NEDA 1 1 6 -1.392255 -0.678756 1.337814 6 -0.386290 0.265087 1.574219 6 -0.560244 1.588211 1.067178 6 -2.676093 0.678261 0.141222 6 0.254261 -1.510296 2.543839 1 0.802057 -2.237275 3.121360 7 -2.537965 -0.538768 0.617800 7 -3.710183 0.954240 -0.727682 1 -4.460845 0.281581 -0.648995 1 -4.050601 1.905534 -0.737736 7 -1.770717 1.690298 0.357510 1 -1.905091 2.586912 -0.096518 7 0.640201 -0.261132 2.323613 7 -0.961955 -1.806816 1.977450 1 -1.452645 -2.688305 2.016474 8 0.194171 2.574460 1.143235 1 -2.428396 -1.911242 -1.824336 7 -1.534411 -2.349247 -1.999555 6 -0.441612 -1.644764 -1.562766 1 -1.506287 -3.316331 -1.709549 7 0.546130 -2.249385 -0.938454 7 -0.438564 -0.300757 -1.892957 6 1.564948 -1.402244 -0.643686 6 0.560094 0.618240 -1.559197 1 -1.204522 0.064228 -2.449766 6 1.625022 -0.032068 -0.867509 7 2.719336 -1.686365 0.037537 8 0.459130 1.830307 -1.833484 7 2.767091 0.521945 -0.337527 6 3.400666 -0.511995 0.207100 1 3.011168 -2.600550 0.352694 1 4.345759 -0.463764 0.721551 11 1.990842 2.827721 -0.234238 $NBO $END $DEL NEDA END $END but in my output file I'm finding only the normal NBO analysis without the energy decomposition results. Could anyone of you kindly suggest me how to change the input file to get the desired result? I have one more question- whether NBO version 3.1 (or any other higher version) comes embedded with gaussian 03 package (or G09 etc;) or do we need to buy it separately? thanks. regards Sagarika From owner-chemistry@ccl.net Wed Aug 18 09:23:01 2010 From: "Andras Borosy andras.borosy[A]givaudan.com" To: CCL Subject: CCL: AW: computer aided organic synthesis Message-Id: <-42553-100818030721-19079-d3nIV0Yg22fYFJjKtrB6kw*o*server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 0027191BC1257783_=" Date: Wed, 18 Aug 2010 09:07:11 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy*|*givaudan.com] This is a multipart message in MIME format. --=_alternative 0027191BC1257783_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable ArChem: Automating Retrosynthetic Chemistry http://www.simbiosys.ca/archem/index.html Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Wolf-D. Ihlenfeldt wdi^^^xemistry.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com.:.ccl.net 17.08.2010 16:30 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: AW: computer aided organic synthesis Theresa: =20 http://www.molecular-networks.com/products/theresa =20 =20 =20 Von: owner-chemistry+wdi=3D=3Dxemistry.com%%ccl.net=20 [mailto:owner-chemistry+wdi=3D=3Dxemistry.com%%ccl.net] Im Auftrag von jale= el=20 uc jaleel.uc[]gmail.com Gesendet: Dienstag, 17. August 2010 13:19 An: Ihlenfeldt, Wolf D=20 Betreff: CCL: computer aided organic synthesis =20 Dear all=20 =20 =20 can you sugget me a software for computer aided organic synthesis=20 =20 Thanks --=20 Dr U.C.A.Jaleel. Asst Professor in cheminformatics=20 Cheminformatics Division( UGC) Malabar Christian College=20 Calicut University --=_alternative 0027191BC1257783_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
ArChem: Automating Retrosynthetic Ch= emistry

http://www.simbiosys.ca/archem/index= .html

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com



"Wolf-D. Ihlenfe= ldt wdi^^^xemistry.com" <owner-chemistry.:.ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com.:.ccl.net

17.08.2010 16:30
Please respond to
"CCL Subscribers" <chemistry.:.ccl.net>
To
"Borosy, Andras " <andras.borosy.:.givaudan.com>
cc
Subject
CCL: AW: computer aided organic synt= hesis





Theresa:
 
http://www.molecular-networks.com/p= roducts/theresa
 
 
 
Von: owner-chemistry+wdi=3D=3Dxem= istry.com%%ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com%%ccl.net] Im Auftrag von <= /b>jaleel uc jaleel.uc[]gmail.com
Gesendet: Dienstag, 17. August 2010 13:19
An: Ihlenfeldt, Wolf D
Betreff: CCL: computer aided organic synthesis
 
Dear all
 
 
can you sugget me a software for computer aided organic synthesis
 
Thanks

--
Dr U.C.A.Jaleel.
Asst Professor in cheminformatics
Cheminformatics Division( UGC)
Malabar Christian College
Calicut University
--=_alternative 0027191BC1257783_=-- From owner-chemistry@ccl.net Wed Aug 18 09:58:01 2010 From: "Andreas Klamt klamt+/-cosmologic.de" To: CCL Subject: CCL:G: COSMO-RS, enthalpy and free energy of complexation Message-Id: <-42554-100818042611-1947-7ldbAYvcmsK+aRKauHrZAA#server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 18 Aug 2010 10:25:30 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt|-|cosmologic.de] Dear Sayed, since I was in holidays, I am answering delayed: Let me first say that your are not using COSMO-RS in Gaussian, but just used the keyword COSMO-RS!!!. Gaussian never had a COSMO-RS module. It just had a COSMO-RS, which did the settings of C-PCM in a way, that it finally was writing COSMO files, which could be post-processed by our COSMO-RS program COSMOtherm. COSMO-RS itself is a thermodynamic postprocessing of COSMO calculations for solutes and solvents, which yields the chemical potential of the almost arbitrary solvutes X in pure and mixed solvents as a function of concentration and temperature. For more information about COSMO-RS see our homepage www.cosmologic.de, or my book "COSMO-RS: > From quantum chemistry to fluid phase thermodynamics and drug design", Elsevier, 2005. Regarding your questions: 1) Yes, the scenario seems to be right, if the the metal in the metal-ligand is no longer solvent exposed, and if your metal-water cluster is sufficiently large to prevent solvent exposition of the metal. I am not sure whether 4 waters are enough. 2) You need to do geometry optimization in solution separately! At the end you should follow the scheme for reaction calculations, which I proposed several times here in CCL, i.e. - calculate the gasphase reaction at high level, incl. vibr. corrections. - add dG of solvation (from COSMO-RS or from another solvation model) for educts and products - for dH do the same, i.e. first calculate it in the gasphase and then take dH of solvation from COSMO-RS and add it on both sides. Please note that only COSMO-RS gives both, dG and dH od solvation separately. Other solvation models just give dG of solvation. Please also note, that by calculating vibrational corrections explicitly in solution does not work, as pointed out a few times in CCL. Regards Andreas Am 18.08.2010 00:43, schrieb Sayed Mesa elsayed.elmes[*]yahoo.com: > Sent to CCL by: "Sayed Mesa" [elsayed.elmes**yahoo.com] > Dear All, > A couple of days ago, I sent to inquire about COSMO-RS, please see below: > Could anybody kindly answer this inquiry? > --------------------------------------------------------------------- > I am calculating the enthalpy and free energy for complexation reaction between transition metal with chelate ligand (has four N-atoms for coordination) in both gas phase and solvent (COSMO-RS). In both cases I used tetrasolvated cluster of water molecules around the transition metal (i.e. bare metal is not used). So the reaction will be: > > L + [M(H2O)4]2+ ---- [ML]2+ + 4H2O (either in gas or in solvent). > > I have two questions; the first: is this scenario is right? If yes please confirm me by a reference if possible. The second question, is I need to do geometry optimization for reactants and products again in solvent or single point calculations is enough for calculating the enthalpy and free energy for complexation? > > Thanks in advance > Sayed> > > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt_-_cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Aug 18 11:18:02 2010 From: "Sergio Emanuel Galembeck segalemb{=}usp.br" To: CCL Subject: CCL:G: NEDA Analysis with NBO keyword in Gaussian03 Message-Id: <-42555-100818102234-26284-jG+2aJsEGotFu9VG/hR7PA|*|server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 18 Aug 2010 11:22:23 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb*usp.br] Dear Sagarita, It is only possible to make NEDA by NBO 5.0, that is not part of Gxx. You will need to buy it and interface with Gaussian program. Best regards, Sergio Citando "Sagarika Dev sagarika.dev__gmail.com" : > > Sent to CCL by: "Sagarika Dev" [sagarika.dev%a%gmail.com] > Dear All, > I was trying to do Natural energy decomposition analysis for a > trimer using NBO key word in Gaussian03. I am attaching below the > sample input file > %chk=gt2_neda.chk > %mem=2GB > %nprocshared=2 > # HF/6-31g(d,p) pop=nboread > > gt2 NEDA > > 1 1 > 6 -1.392255 -0.678756 1.337814 > 6 -0.386290 0.265087 1.574219 > 6 -0.560244 1.588211 1.067178 > 6 -2.676093 0.678261 0.141222 > 6 0.254261 -1.510296 2.543839 > 1 0.802057 -2.237275 3.121360 > 7 -2.537965 -0.538768 0.617800 > 7 -3.710183 0.954240 -0.727682 > 1 -4.460845 0.281581 -0.648995 > 1 -4.050601 1.905534 -0.737736 > 7 -1.770717 1.690298 0.357510 > 1 -1.905091 2.586912 -0.096518 > 7 0.640201 -0.261132 2.323613 > 7 -0.961955 -1.806816 1.977450 > 1 -1.452645 -2.688305 2.016474 > 8 0.194171 2.574460 1.143235 > 1 -2.428396 -1.911242 -1.824336 > 7 -1.534411 -2.349247 -1.999555 > 6 -0.441612 -1.644764 -1.562766 > 1 -1.506287 -3.316331 -1.709549 > 7 0.546130 -2.249385 -0.938454 > 7 -0.438564 -0.300757 -1.892957 > 6 1.564948 -1.402244 -0.643686 > 6 0.560094 0.618240 -1.559197 > 1 -1.204522 0.064228 -2.449766 > 6 1.625022 -0.032068 -0.867509 > 7 2.719336 -1.686365 0.037537 > 8 0.459130 1.830307 -1.833484 > 7 2.767091 0.521945 -0.337527 > 6 3.400666 -0.511995 0.207100 > 1 3.011168 -2.600550 0.352694 > 1 4.345759 -0.463764 0.721551 > 11 1.990842 2.827721 -0.234238 > > $NBO $END > $DEL > NEDA END > $END > > but in my output file I'm finding only the normal NBO analysis > without the energy decomposition results. Could anyone of you kindly > suggest me how to change the input file to get the desired result? > > I have one more question- whether NBO version 3.1 (or any other > higher version) comes embedded with gaussian 03 package (or G09 > etc;) or do we need to buy it separately? > > thanks. > > regards > Sagarika> > > From owner-chemistry@ccl.net Wed Aug 18 11:53:01 2010 From: "John McKelvey jmmckel_._gmail.com" To: CCL Subject: CCL: COSMO-RS, enthalpy and free energy of complexation Message-Id: <-42556-100818101657-20929-8uvwtQyoolytcVgiM9JNvQ[]server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 18 Aug 2010 10:16:48 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel,+,gmail.com] I certainly am no expert on this, but first, when investigating reaction energies geometries should be optimized and zero-point point vibrational energies should be computed. As to COSMO-RS, special software from Andreas Klamt at Klamt:_:Cosmologic.de is needed. (I forwarded your original message to him but he is traveling and will likely get back to you later.) However, COSMO solvation energies can be computed in several programs; the program(s) available to you is not stated. Best regards, John McKelvey. On Tue, Aug 17, 2010 at 6:43 PM, Sayed Mesa elsayed.elmes[*]yahoo.com wrote: > > Sent to CCL by: "Sayed  Mesa" [elsayed.elmes**yahoo.com] > Dear All, > A couple of days ago, I sent to inquire about COSMO-RS, please see below: > Could anybody kindly answer this inquiry? > --------------------------------------------------------------------- > I am calculating the enthalpy and free energy for complexation reaction between transition metal with chelate ligand (has four N-atoms for coordination) in both gas phase and solvent (COSMO-RS). In both cases I used tetrasolvated cluster of water molecules around the transition metal (i.e. bare metal is not used). So the reaction will be: > > L +  [M(H2O)4]2+  ---- [ML]2+    + 4H2O      (either in gas or in solvent). > > I have two questions; the first: is this scenario is right? If yes please confirm me by a reference if possible. The second question, is I need to do geometry optimization for reactants and products again in solvent or single point calculations is enough for calculating the enthalpy and free energy for complexation? > > Thanks in advance > Sayed>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel:_:gmail.com From owner-chemistry@ccl.net Wed Aug 18 12:27:02 2010 From: "Lochana C Menikarachchi lochanac!^!yahoo.com" To: CCL Subject: CCL: HIPS library Message-Id: <-42557-100818113644-30788-tVGtrsVZdj8ck9dqQyAysA(-)server.ccl.net> X-Original-From: "Lochana C Menikarachchi" Date: Wed, 18 Aug 2010 11:36:42 -0400 Sent to CCL by: "Lochana C Menikarachchi" [lochanac.,+,.yahoo.com] Does Anybody have experience with HIPS library. I was trying to run the modified testHIPS1.ex given in the PARALLEL folder with verysmall.mtx matrix with 1s in the rhs file. The answer does not match with the mathematica answer which is correct. Thanks. From owner-chemistry@ccl.net Wed Aug 18 13:03:01 2010 From: "Nuno A. G. Bandeira nuno.bandeira]-[ist.utl.pt" To: CCL Subject: CCL: NEDA Analysis with NBO keyword in Gaussian03 Message-Id: <-42558-100818103635-9852-8qW4va+Oe/qbU1MzDUodJw__server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Wed, 18 Aug 2010 15:36:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira\a/ist.utl.pt] Dear Sagarika, The NBO manual states that NEDA is only available with the GAMESS program after recompiling from the NBO source. Best wishes, Nuno -- Nuno A. G. Bandeira, AMRSC Laboratoire de Chimie LR6 Ecole Normale Superieure de Lyon 46, Allee d'Italie 69364 Lyon Cedex 07 - France http://cqb.fc.ul.pt/intheochem/nuno/ -- From owner-chemistry@ccl.net Wed Aug 18 13:38:02 2010 From: "Sagarika Dev sagarika.dev/./gmail.com" To: CCL Subject: CCL:G: NEDA Analysis with NBO keyword in Gaussian03 Message-Id: <-42559-100818131419-325-VHboCs/mhQEb1YM7a1hs/Q-#-server.ccl.net> X-Original-From: "Sagarika Dev" Date: Wed, 18 Aug 2010 13:14:16 -0400 Sent to CCL by: "Sagarika Dev" [sagarika.dev++gmail.com] Dear Sergio, Thanks a load for your kind reply. I have Gaussian03, hence do I need to buy NBO5.G or NBO5.0? Could you please tell me step by step how to interface NBO5.0G with gaussian03 or should I get the information with the CD that I shall buy? regards Sagarika From owner-chemistry@ccl.net Wed Aug 18 14:13:01 2010 From: "Sayed Mesa elsayed.elmes]|[yahoo.com" To: CCL Subject: CCL:G: COSMO-RS, enthalpy and free energy of complexation Message-Id: <-42560-100818134025-25726-893QHogO/eTrZvmpWAiUOw[#]server.ccl.net> X-Original-From: "Sayed Mesa" Date: Wed, 18 Aug 2010 13:40:09 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes*yahoo.com] Dear Andreas, John and all I am very thankful for wise answer from Andreas. Also, I would like to thank John. I have still question about how can I know 4 waters molecules are enough to form metal-water cluster? I looked for literature and I found a related paper: "Ab Initio Study of M+:18-Crown-6 Microsolvation" J. Phys. Chem. A 1997, 101, 2723-2731. Unfortunately, studied metals in this paper do not include transition metal. For transition metal like Zn (II) or Ni (II) how can I define number of solvated water molecules? Thanks in advance Sayed ------------------------------------ >Sent to CCL by: John McKelvey [jmmckel,+,gmail.com] I certainly am no expert on this, but first, when investigating reaction energies geometries should be optimized and zero-point point vibrational energies should be computed. As to COSMO-RS, special software from Andreas Klamt at Klamt(-)Cosmologic.de is needed. (I forwarded your original message to him but he is traveling and will likely get back to you later.) However, COSMO solvation energies can be computed in several programs; the program(s) available to you is not stated. Best regards, John McKelvey. ---------------------------------------- >Sent to CCL by: Andreas Klamt [klamt|-|cosmologic.de] Dear Sayed, since I was in holidays, I am answering delayed: Let me first say that your are not using COSMO-RS in Gaussian, but just used the keyword COSMO-RS!!!. Gaussian never had a COSMO-RS module. It just had a COSMO-RS, which did the settings of C-PCM in a way, that it finally was writing COSMO files, which could be post-processed by our COSMO-RS program COSMOtherm. COSMO-RS itself is a thermodynamic postprocessing of COSMO calculations for solutes and solvents, which yields the chemical potential of the almost arbitrary solvutes X in pure and mixed solvents as a function of concentration and temperature. For more information about COSMO-RS see our homepage www.cosmologic.de, or my book "COSMO-RS: > From quantum chemistry to fluid phase thermodynamics and drug design", Elsevier, 2005. Regarding your questions: 1) Yes, the scenario seems to be right, if the the metal in the metal-ligand is no longer solvent exposed, and if your metal-water cluster is sufficiently large to prevent solvent exposition of the metal. I am not sure whether 4 waters are enough. 2) You need to do geometry optimization in solution separately! At the end you should follow the scheme for reaction calculations, which I proposed several times here in CCL, i.e. - calculate the gasphase reaction at high level, incl. vibr. corrections. - add dG of solvation (from COSMO-RS or from another solvation model) for educts and products - for dH do the same, i.e. first calculate it in the gasphase and then take dH of solvation from COSMO-RS and add it on both sides. Please note that only COSMO-RS gives both, dG and dH od solvation separately. Other solvation models just give dG of solvation. Please also note, that by calculating vibrational corrections explicitly in solution does not work, as pointed out a few times in CCL. Regards Andreas From owner-chemistry@ccl.net Wed Aug 18 14:48:01 2010 From: "Methai DC mdccompchem^_^gmail.com" To: CCL Subject: CCL: Spin density Message-Id: <-42561-100818134405-29975-JjU6Jq1y6KP6D0u2BCVKlg-.-server.ccl.net> X-Original-From: Methai DC Content-Type: multipart/alternative; boundary=0016e64bdf5407415e048e1c9c3c Date: Wed, 18 Aug 2010 23:13:54 +0530 MIME-Version: 1.0 Sent to CCL by: Methai DC [mdccompchem**gmail.com] --0016e64bdf5407415e048e1c9c3c Content-Type: text/plain; charset=ISO-8859-1 Dear All, I am new in the field of computational chemistry. So please help me in following regard: How to generate SPIN DENSITY PLOT? Is it possible to generate using Chemcraft? Or any different software is needed? What is the procedure? Many thanks in advance. Sincerely, Moumita --0016e64bdf5407415e048e1c9c3c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,
=A0=A0 I am new in the field of computational chemistry. So pl= ease help me in following regard: How to generate SPIN DENSITY PLOT? Is it = possible to generate using Chemcraft? Or any different software is needed? = What is the procedure?

Many thanks in advance.

Sincerely,
Moumita
--0016e64bdf5407415e048e1c9c3c-- From owner-chemistry@ccl.net Wed Aug 18 17:23:00 2010 From: "Wo Agnessi witch.of.agnessi^gmail.com" To: CCL Subject: CCL: How to extract half of a C2 symmetric homodimer complex Message-Id: <-42562-100818163009-32048-9PcOrK2zyLmdHhbN1FNiHA\a/server.ccl.net> X-Original-From: "Wo Agnessi" Date: Wed, 18 Aug 2010 16:30:07 -0400 Sent to CCL by: "Wo Agnessi" [witch.of.agnessi(a)gmail.com] Hello, The homodimers I'm working with are C2 symmetric and thus have ying-yang type structure. Simply put the head (H) region of one subunit interacts with the tail (T) region of the other subunit and vice-versa. I need to extract the coordinates of just half of a symmetric complex, ie.the coords of H region from one subunit along with the T region of the other. Pictorially, | H-T H | T : : ==> : | : T-H T | H | Please note that the complexes are NOT absolutely symmetric, even though they are homodimers. Differences in Side chain and even some backbone conformations are present. I' m not sure how to find out the plane that breaks the molecule to two HT halves. Can anybody tell me if there are some softwares to do it, or point to the theory/literature, so that I can write a script. Thanks in advance From owner-chemistry@ccl.net Wed Aug 18 17:58:02 2010 From: "Theodore S. Dibble tsdibble###syr.edu" To: CCL Subject: CCL: adiabatic ionization potential and adiabatic ionization energy Message-Id: <-42563-100818152239-6207-Bred89wwmnev8sg/AZCy/A[*]server.ccl.net> X-Original-From: "Theodore S. Dibble" Date: Wed, 18 Aug 2010 15:22:33 -0400 Sent to CCL by: "Theodore S. Dibble" [tsdibble]^[syr.edu] "Ionization potential" is just an older term for "ionization energy." See http://en.wikipedia.org/wiki/Ionization_energy. So the two quantities you are asking about are the same. - Ted Dibble > "Ba Tai Truong Truong.BaTai**chem.kuleuven.be" wrote: > > Sent to CCL by: Ba Tai Truong [Truong.BaTai###chem.kuleuven.be] > Dear CCL members > > Could you tell exactly what is difference between the adiabatic ionization potential and adiabatic ionization energy?