From owner-chemistry@ccl.net Tue May 7 08:06:01 2013 From: "=?ISO-8859-1?Q?Jo=E3o_Brand=E3o?= jbrandao/a\ualg.pt" To: CCL Subject: CCL: O(3P) vs. O(1S) Message-Id: <-48649-130506102535-1410-VgvqL1QJO2061lfbZOk+Sg|*|server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Jo=E3o_Brand=E3o?= Content-Type: multipart/alternative; boundary="------------040205080502020306040504" Date: Mon, 06 May 2013 15:25:16 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Jo=E3o_Brand=E3o?= [jbrandao],[ualg.pt] This is a multi-part message in MIME format. --------------040205080502020306040504 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit As said Tennyson: Hund's rule says that for open shell many electron atoms the state with largest total spin is more stable. This result comes from the antisymmetry of the total wavefunction. It is difficult to show for many-electron atoms, but for a two electron system we can separate the spacial and spin parts of the wave function and the triplet wave function becomes zero when the two electrons approach each other (this is called the Fermi hole). As a consequence the electronic repulsion is lower for the triplet state. You can easily find animations of the fermi-hole in the internet. Things are still more complicated and, due to spin-orbit coupling, the (3P) state has three different energies. Regards João Brandão Em 05-05-2013 08:44, bonoit bonoit bonoit_10---yahoo.fr escreveu: > Sent to CCL by: "bonoit bonoit" [bonoit_10,,yahoo.fr] > Dear CCLers, > > I would like to enquire about the oxygen atom. Why this atom prefer the triplet state O(3P) to the singlet one? Is it just a matter of stability or is there any other reason? > > Regards > Bonoit> > > > --------------040205080502020306040504 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit As said Tennyson: Hund's rule says that for open shell many electron atoms the state with largest total spin is more stable.

This result comes from the antisymmetry of the total wavefunction.
It is difficult to show for many-electron atoms, but for a two electron system we can separate the spacial and spin parts of the wave function and the triplet wave function becomes zero when the two electrons approach each other (this is called the Fermi hole). As a consequence the electronic repulsion is lower for the triplet state.
You can easily find animations of the fermi-hole in  the internet.

Things are still more complicated and, due to spin-orbit coupling, the (3P) state has three different energies.

Regards

João Brandão



 


Em 05-05-2013 08:44, bonoit bonoit bonoit_10---yahoo.fr escreveu: 
Sent to CCL by: "bonoit  bonoit" [bonoit_10,,yahoo.fr]
Dear CCLers,

I would like to enquire about the oxygen atom. Why this atom prefer the triplet state O(3P) to the singlet one? Is it just a matter of stability or is there any other reason?

Regards
BonoitE-mail to subscribers: CHEMISTRY .. ccl.net or use:
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--------------040205080502020306040504-- From owner-chemistry@ccl.net Tue May 7 08:41:00 2013 From: "Antarip Halder antarip.halder,gmail.com" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48650-130507015057-5383-Rr4o5aWi4ZjsqLT0dVNTgw++server.ccl.net> X-Original-From: Antarip Halder Content-Type: multipart/alternative; boundary=047d7b86e7723a3ea204dc1a66dd Date: Tue, 7 May 2013 11:20:29 +0530 MIME-Version: 1.0 Sent to CCL by: Antarip Halder [antarip.halder]|[gmail.com] --047d7b86e7723a3ea204dc1a66dd Content-Type: text/plain; charset=ISO-8859-1 Dear All, I am trying to calculate the dipole moment of charged species using Gaussian and I have to compare dipole moments of different singly charged species. I am aware of the fact that dipole moment for the molecular species which have non zero charge is not defined. The comparison can be performed only in the case when the position of coordinate origin is not changed. Can any one tell me how can I define the origin to calculate the dipole moment. Thanks in advance. Antarip Halder MS by Research Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology, Hyderabad Andhra Pradesh, India -- If you think you can, you are right. -- If you think you can, you are right. --047d7b86e7723a3ea204dc1a66dd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,
<= div>
I am trying to calculate the dipole moment of charged species using= Gaussian and I have to compare dipole moments of different singly charged = species. I am aware of the fact that dipole moment for the molecular species which have no= n zero charge is not defined. The comparison can be performed only in the c= ase when the position of coordinate origin is not changed.

Can any one tell me how can I define the origin to calc= ulate the dipole moment.=A0

Thanks in advance.
Antarip Halder
MS by Research
Center for Computational Natural Sciences and Bioinformatics
Inte= rnational Institute of Information Technology, Hyderabad
Andhra P= radesh, India
--
If you think you can, you are right.



--
If you think you can, you= are right.
--047d7b86e7723a3ea204dc1a66dd-- From owner-chemistry@ccl.net Tue May 7 11:23:01 2013 From: "Cina Foroutan-Nejad canyslopus-x-yahoo.co.uk" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48651-130507101317-17306-E1vZ0qvwVvX1WHhJzSNN1g__server.ccl.net> X-Original-From: Cina Foroutan-Nejad Content-Type: multipart/alternative; boundary="1453005445-1488537443-1367935988=:82516" Date: Tue, 7 May 2013 15:13:08 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Cina Foroutan-Nejad [canyslopus.{:}.yahoo.co.uk] --1453005445-1488537443-1367935988=:82516 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Antarip,=0A=0AYou are right, dipole moment for charged systems is an i= ll-defined quantity as it is gauge-dependent. If your molecules are differe= nt i.e. number or=A0arrangement=A0of atoms are different it is better to fo= rget about any direct=A0comparison! I suggest that you add counter ions and= measure the dipole moment in the presence of those counter ions. Neverthel= ess, counter ions almost always accompany a charged system. If you are real= ly interested to measure the dipole moment for your systems without counter= ions then I suggest to first add some counter ions, then optimize your mol= ecules in the presence of them and prepare wavefunction (WFN) files. You ca= n analyze the WFNs by QTAIM and separate the atomic moment of the counter i= ons from the total moment. The remaining moment is dipole of your charged s= ystem. Now, it is not gauge dependent!=0A=0AGood luck,=0ACina=0A+++++++++++= ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=0ACina= Foroutan-Nejad, Ph.D.=0Ahttp://muni.academia.edu/CinaForoutanNejad=0A=0A= =0A=0A________________________________=0A From: "Antarip Halder antarip.hal= der,gmail.com" =0ATo: "Foroutan-Nejad, Cina -id#47= z-" =0ASent: Tuesday, 7 May 2013, 7:50=0ASubject: = CCL:G: Dipole moment of charged species in Gaussian=0A =0A=0A=0ADear All,= =0A=0A=0AI am trying to calculate the dipole moment of charged species usin= g Gaussian and I have to compare dipole moments of different singly charged= species. I am aware of the fact that dipole moment for the molecular speci= es which have non zero charge is not defined. The comparison can be perform= ed only in the case when the position of coordinate origin is not changed.= =0A=0ACan any one tell me how can I define the origin to calculate the dipo= le moment.=A0=0A=0AThanks in advance.Antarip Halder=0AMS by Research=0ACent= er for Computational Natural Sciences and Bioinformatics=0AInternational In= stitute of Information Technology, Hyderabad=0AAndhra Pradesh, India-- =0AI= f you think you can, you are right.=0A=0A=0A=0A-- =0AIf you think you can, = you are right. --1453005445-1488537443-1367935988=:82516 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Antarip,

You are right, dipole moment fo= r charged systems is an ill-defined quantity as it is gauge-dependent. If y= our molecules are different i.e. number or arrangement of atoms a= re different it is better to forget about any direct comparison! I sug= gest that you add counter ions and measure the dipole moment in the presenc= e of those counter ions. Nevertheless, counter ions almost always accompany= a charged system. If you are really interested to measure the dipole momen= t for your systems without counter ions then I suggest to first add some cou= nter ions, then optimize your molecules in the presence of them and prepare= wavefunction (WFN) files. You can analyze the WFNs by QTAIM and separate t= he atomic moment of the counter ions from the total moment. The remaining m= oment is dipole of your charged system. Now, it is not gauge dependent!

Good luck= ,
Cina
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++= ++++++++++++++++++++
Cina Foroutan-Nejad, P= h.D.
http://muni.academia.edu/CinaForoutanNejad
<= /div>

From: "Antarip Halder antarip.halder,gmai= l.com" <owner-chemistry{:}ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus{:}yahoo.c= o.uk>
Sent: Tuesda= y, 7 May 2013, 7:50
Subject: CCL:G: Dipole moment of charged species in Gaussian

Dear All,

I am trying to calculate the dipole moment of charged species usi= ng Gaussian and I have to compare dipole moments of different singly charge= d species. I am aware of the fact that dipole moment for the molecular species which have non zero charge i= s not defined. The comparison can be performed only in the case when the po= sition of coordinate origin is not changed.
=0A=0A=0A

<= /div>
Can any one tell me how can I define the origin to calculate the = dipole moment. 

Thanks in advance.
Antarip Ha= lder
=0A=0A
MS by Research
=0ACenter for Computational N= atural Sciences and Bioinformatics
International Institute of Inf= ormation Technology, Hyderabad
Andhra Pradesh, India
--
= If you think you can, you are right.
=0A=0A
=0A=



--
If you think you can, you= are right.
=0A


--1453005445-1488537443-1367935988=:82516-- From owner-chemistry@ccl.net Tue May 7 12:41:01 2013 From: "Reis Heribert hreis_-_eie.gr" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48652-130507122614-15680-Vxvhh/a4HAixAMBuAr3i4w{=}server.ccl.net> X-Original-From: Reis Heribert Content-Type: multipart/alternative; boundary=047d7b86e3a84dba6a04dc2346df Date: Tue, 7 May 2013 18:26:08 +0200 MIME-Version: 1.0 Sent to CCL by: Reis Heribert [hreis---eie.gr] --047d7b86e3a84dba6a04dc2346df Content-Type: text/plain; charset=ISO-8859-1 Hello The definition of the dipole moment of a charged species is well defined. The only problem with it (and with all higher multipoles) is, that its value depends on the origin of the coordinate system. Thus for comparison purposes the origin of the coordinate system of different molecules should be comparable. A very common choice is the centre of mass; another possibility is the center of nuclear charge, which is the standard origin in Gaussian09, if one does not specify the 'Nosymm' keyword. You can also turn the problem on its head and define the origin as that point where the dipole is zero... I'm assuming that you want to compare the absolute value of the dipole between different molecules. In case you also want to compare the components, you also should use comparable orientations of the coordinate systems (e.g the coordinate system where e.g. the inertia (or polarizability or ...) tensor is diagonal). This, however, is independent of being charged or uncharged. Heribert --047d7b86e3a84dba6a04dc2346df Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello

The definition of the di= pole moment of a charged species is well defined. The only problem with it = (and with all higher multipoles) is, that its value depends on the origin o= f the coordinate system. Thus for comparison purposes the origin of the coo= rdinate system of different molecules should be comparable. A very common c= hoice is the centre of mass; another possibility is the center of nuclear c= harge, which is the standard origin in Gaussian09, if one does not specify = the 'Nosymm' keyword. You can also turn the problem on its head and= define the origin as that point where the dipole is zero...

I'm assuming that you want to compare the absolute value of t= he dipole between different molecules. In case you also want to compare the= components, you also should use comparable orientations of the coordinate = systems (e.g the coordinate system where e.g. the inertia (or polarizabilit= y or ...) tensor is diagonal). This, however, is independent of being charg= ed or uncharged.

Heribert
--047d7b86e3a84dba6a04dc2346df-- From owner-chemistry@ccl.net Tue May 7 13:15:00 2013 From: "Igor Filippov igor.v.filippov-*-gmail.com" To: CCL Subject: CCL: osra 2.0.0 release Message-Id: <-48653-130507125749-29232-fXocy3MU7TAJ4JU0SmIM6Q]^[server.ccl.net> X-Original-From: Igor Filippov Content-Type: multipart/alternative; boundary=047d7b343b942a496104dc23b783 Date: Tue, 7 May 2013 12:57:41 -0400 MIME-Version: 1.0 Sent to CCL by: Igor Filippov [igor.v.filippov+*+gmail.com] --047d7b343b942a496104dc23b783 Content-Type: text/plain; charset=ISO-8859-1 Dear Colleagues, We are glad to announce the release of Optical Structure Recognition Application OSRA 2.0.0. Among the improvements in the new version: - Significantly improved recognition rates: https://sourceforge.net/apps/mediawiki/osra/index.php?title=Validation - Added recognition of Iodine, wavy bonds, etc. - Completely modified confidence function (values not compatible with the earlier versions). - Updated table detection and removal routines. - Created binary package for Linux (statically linked, should work on all modern Linux systems). - Windows and Mac OSX versions now support multi-threading processing of PDF files. With this release the distribution model has been changed a bit: while the source code is available free as before, to offset the development costs the installable packages for Windows, Mac OSX and Linux can be purchased for a fee. You can find the download links at http://osra.sf.net Best regards, Igor Filippov --047d7b343b942a496104dc23b783 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

We are glad= to announce the release of Optical Structure Recognition Application
=
OSRA 2.0.0. Among the improvements in the new version:



- Added recognition of Iodine, wavy bonds, etc.

- Completely modified confidence function (values not com= patible with the earlier versions).

- Updated tabl= e detection and removal routines.

- Created binary package for Linux (statically linked, = should work on all modern Linux systems).

- Window= s and Mac OSX versions now support multi-threading processing of PDF files.= =A0

With this release the distribution model has been chang= ed a bit: while the source code is
available free as before, to o= ffset the development costs the installable packages for Windows,
Mac OSX and Linux can be purchased for a fee. You can find the downloa= d links
at http://osra.sf.net<= /div>

Best regards,
Igor Filippov
--047d7b343b942a496104dc23b783-- From owner-chemistry@ccl.net Tue May 7 20:12:00 2013 From: "John McKelvey jmmckel===gmail.com" To: CCL Subject: CCL:G: Dipole moment of charged species in Gaussian Message-Id: <-48654-130507145401-11745-bwF7yAlEZ5fuJ3+N+q68iQ{}server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=f46d043c07e0cda4f204dc2556d7 Date: Tue, 7 May 2013 14:53:54 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel~~gmail.com] --f46d043c07e0cda4f204dc2556d7 Content-Type: text/plain; charset=ISO-8859-1 Hello, Perhaps there is another way to look at it, and it is a subset of looking at the center of nuclear charge. Perhaps it is more sensitive (?) to look at the center of constituent free atom valence electrons? John McKelvey On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr < owner-chemistry:-:ccl.net> wrote: > Hello > > The definition of the dipole moment of a charged species is well defined. > The only problem with it (and with all higher multipoles) is, that its > value depends on the origin of the coordinate system. Thus for comparison > purposes the origin of the coordinate system of different molecules should > be comparable. A very common choice is the centre of mass; another > possibility is the center of nuclear charge, which is the standard origin > in Gaussian09, if one does not specify the 'Nosymm' keyword. You can also > turn the problem on its head and define the origin as that point where the > dipole is zero... > > I'm assuming that you want to compare the absolute value of the dipole > between different molecules. In case you also want to compare the > components, you also should use comparable orientations of the coordinate > systems (e.g the coordinate system where e.g. the inertia (or > polarizability or ...) tensor is diagonal). This, however, is independent > of being charged or uncharged. > > Heribert > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel:-:gmail.com --f46d043c07e0cda4f204dc2556d7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello,

Perhaps there is another way= to look at it, and it is a subset of looking at the center of nuclear char= ge.=A0 Perhaps it is more sensitive (?) to look at the center of=A0 constit= uent free atom valence electrons?

John McKelvey


On Tue, May 7, 2013 at 12:26 PM, Reis Heribert hreis_-_eie.gr <owner-chemistry:-:ccl.n= et> wrote:
Hello
The definition of the dipole moment of a charged species is well def= ined. The only problem with it (and with all higher multipoles) is, that it= s value depends on the origin of the coordinate system. Thus for comparison= purposes the origin of the coordinate system of different molecules should= be comparable. A very common choice is the centre of mass; another possibi= lity is the center of nuclear charge, which is the standard origin in Gauss= ian09, if one does not specify the 'Nosymm' keyword. You can also t= urn the problem on its head and define the origin as that point where the d= ipole is zero...

I'm assuming that you want to compare the absolute value of t= he dipole between different molecules. In case you also want to compare the= components, you also should use comparable orientations of the coordinate = systems (e.g the coordinate system where e.g. the inertia (or polarizabilit= y or ...) tensor is diagonal). This, however, is independent of being charg= ed or uncharged.

Heri= bert



--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel:-:gmail.com
--f46d043c07e0cda4f204dc2556d7--