From owner-chemistry@ccl.net Mon Mar 8 10:04:01 2010 From: "Taye Beyene D sene3095]-[yahoo.com" To: CCL Subject: CCL: Fullerene calculations Message-Id: <-41387-100308100102-7849-g9sKEnK9uqFRADQRa4d2bg]=[server.ccl.net> X-Original-From: "Taye Beyene D" Date: Mon, 8 Mar 2010 10:00:59 -0500 Sent to CCL by: "Taye Beyene D" [sene3095*|*yahoo.com] Hi all, I have built fullerene C60 molecule and I have the cartesian coordinates. But my major aim is to put hydrogen molecule inside the fullerene molecule. When I put it inside the fullerene oppens by removing two carbons from the cage. If you have some solutions please send me an advice. Thank you in advance. From owner-chemistry@ccl.net Mon Mar 8 12:55:01 2010 From: "Jamin Krinsky jamink]-[berkeley.edu" To: CCL Subject: CCL: interpretation the Natural Bond Orbitals (NBO) results Message-Id: <-41388-100308122419-1927-FePb7F7dQfjC0zgODhJWkw-,-server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=0016363ba1aef7629404814d54db Date: Mon, 8 Mar 2010 09:24:04 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink(_)berkeley.edu] --0016363ba1aef7629404814d54db Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear May, NBO constructs a localized set of orbitals (based on atom-centered hybrid AOs) which fall into the categories (at least for closed-shell systems): BD (bonding, 2 electrons significantly shared between two atoms), BD* (antibonding, same as above, but the hybrids are out of phase/antibonding), LP (2 electrons only significantly present on one atom), LP* (same as above but formally empty, can have significant population from delocalization fro= m BD or LP orbitals), and finally RY* which come from your polarization/diffuse functions and shouldn't be significantly populated. You didn't list the other atom in each bond you showed in your post, but it looks like you have one orbital that is technically Ru-Ru bonding but is only 4% on the other Ru3, and a technically antibonding orbital that is mostly on Ru3. The population of one is ca. 0.66 electrons and the other is ca. 0.48 electrons so the net Ru-Ru interaction is basically non-bonding, e.g. there are two non-interacting lone pairs, one on each Ru. They are listed as bonds because the sharing is greater than the cutoff for considering them lone pairs (just barely). You can buy GENNBO5.0 and run an archive file (generated in NBO3) through it, which allows you to do a canonical molecular orbital analysis. Some program packages suck as ADF and Jaguar come with this utility program. Thi= s shows you the contributions of each NBO to the MOs, and breaks down each interaction by % bonding/nonbonding/antibonding. To do this, run NBO3.0 wit= h "pop=3Dnboread" in the Route section and "$nbo archive file=3Dyourfilename = $end" after your molecular spec, custom basis sets, etc. This will generate "yourfilename.47", which you open and edit so the second line reads "$NBO cmo $END. Then run GENNBO on it and you will get a repeat of the NBO output= , but with the CMO section included. As for if NBO is appropriate for metal-metal bonding, that depends on if th= e model chemistry you are using is appropriate for metal-metal bonding, because the NBO analysis is just "reshuffling" the orbitals calculated in your ESS program. Very often those interactions are quite multiconfigurational in character, so HF would fail and DFT would be questionable. Additionally, the NBO formalism is a little vague in some instances with regard to DFT (the 2nd order pert. analysis is suspect for instance) so treat results with a critical eye. Hope this helps somewhat. Regards, Jamin On Sat, Mar 6, 2010 at 2:08 AM, may abdelghani may01dz##yahoo.fr < owner-chemistry*o*ccl.net> wrote: > Dear CCL'ers > > 1. What we mean by the world "antibond BD*" in the output of NBO; or I ha= ve > in my NBO output the flowing sentences: > > 575. (0.66522) BD ( 1)Ru 3-Ru 4 > > ( 4.23%) 0.2056*Ru 3 s( 76.43%)p 0.04( 2.89%)d 0.27( > 20.69%) > > 576. (0.47855) BD*( 1)Ru 3-Ru 4 > > ( 95.77%) 0.9786*Ru 3 s( 76.43%)p 0.04( 2.89%)d 0.27( > 20.69%) > > The question is: I have a bond between the atom Ru3 and Ru4 or not=85what= is > the bonding character of this bond? > > > 2. There is any relationship between the =ABcluster valence electron" con= cept > and the results of =ABNatural Electron Configuration"? > > > 4. In terms of single, double and triple bonds, where we classify that > of non-Lewis-type NBOs : BD*, RY* and LP? > > > 5. Can the version 3 of NBO software, NBO.3, give a credibility descripti= on > of metal-metal bond? > > thank a lot for all, > > > > --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink*o*berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --0016363ba1aef7629404814d54db Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear May,

NBO constructs a localized set of orbitals (based on atom-= centered hybrid AOs) which fall into the categories (at least for closed-sh= ell systems): BD (bonding, 2 electrons significantly shared between two ato= ms), BD* (antibonding, same as above, but the hybrids are out of phase/anti= bonding), LP (2 electrons only significantly present on one atom), LP* (sam= e as above but formally empty, can have significant population from delocal= ization from BD or LP orbitals), and finally RY* which come from your polar= ization/diffuse functions and shouldn't be significantly populated.
You didn't list the other atom in each bond you showed in your post= , but it looks like you have one orbital that is technically Ru-Ru bonding = but is only 4% on the other Ru3, and a technically antibonding orbital that= is mostly on Ru3. The population of one is ca. 0.66 electrons and the othe= r is ca. 0.48 electrons so the net Ru-Ru interaction is basically non-bondi= ng, e.g. there are two non-interacting lone pairs, one on each Ru. They are= listed as bonds because the sharing is greater than the cutoff for conside= ring them lone pairs (just barely).

You can buy GENNBO5.0 and run an archive file (generated in NBO3) throu= gh it, which allows you to do a canonical molecular orbital analysis. Some = program packages suck as ADF and Jaguar come with this utility program. Thi= s shows you the contributions of each NBO to the MOs, and breaks down each = interaction by % bonding/nonbonding/antibonding. To do this, run NBO3.0 wit= h "pop=3Dnboread" in the Route section and "$nbo archive fil= e=3Dyourfilename $end" after your molecular spec, custom basis sets, e= tc. This will generate "yourfilename.47", which you open and edit= so the second line reads "$NBO cmo $END. Then run GENNBO on it and yo= u will get a repeat of the NBO output, but with the CMO section included.
As for if NBO is appropriate for metal-metal bonding, that depends on i= f the model chemistry you are using is appropriate for metal-metal bonding,= because the NBO analysis is just "reshuffling" the orbitals calc= ulated in your ESS program. Very often those interactions are quite multico= nfigurational in character, so HF would fail and DFT would be questionable.= Additionally, the NBO formalism is a little vague in some instances with r= egard to DFT (the 2nd order pert. analysis is suspect for instance) so trea= t results with a critical eye.

Hope this helps somewhat.

Regards,
Jamin



On Sat, Mar 6, 2010 at 2:08 AM, may abdelghani may01d= z##yahoo.fr <owner-chemistry*o*ccl.net> = wrote:

Dea= r CCL'ers

1. = What we mean by the world "antibond BD*" in the output of NBO; or= I have in my NBO output the flowing sentences:

575= . (0.66522) BD ( 1)Ru 3-Ru 4=A0=A0=A0= =A0=A0

<= span style=3D"outline-style: none; line-height: 1.2em;">=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0(=A0=A04.23%)=A0=A0=A00.2056*Ru 3 s( 76.43%)p 0.04(=A0=A02.89%)d 0.27( = 20.69%)

<= span dir=3D"LTR" style=3D"outline-style: none; line-height: 1.2em;">= 576. (0.47855) BD*( 1)Ru 3-Ru 4=A0=A0=A0=A0=A0

<= span dir=3D"LTR" style=3D"outline-style: none; line-height: 1.2em;">= =A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0( 95.77%)=A0=A0=A00.9786*Ru 3 s( 76.43%)p 0.04(=A0=A02.89%)d= 0.27( 20.69%)

Th= e question is: I have a bond between the atom Ru3 and Ru4 or not=85what is = the bonding character of this bond?


2. There is any relationship between the =ABcluster valence electron" = concept and the results of =ABNatural Electron Configuration"?


4. In terms of sin= gle, double and triple bonds, where=A0=A0we classify that of=A0=A0non-Lewis-type NBOs=A0<= span style=3D"outline-style: none; line-height: 1.2em;" lang=3D"EN-US">=A0:= BD*, RY* and LP?


5. = Can the version 3 of NBO software, NBO.3, give a=A0credibility=A0= description of metal-metal bond?

thank a lot for all,




--
Jamin L Krinsky, = Ph.D.
Molecular Graphics and Computation Facility
175 Tan Hall, Unive= rsity of California, Berkeley, CA 94720
jamink*o*berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--0016363ba1aef7629404814d54db-- From owner-chemistry@ccl.net Mon Mar 8 15:30:01 2010 From: "John McKelvey jmmckel() gmail.com" To: CCL Subject: CCL: Fullerene calculations Message-Id: <-41389-100308152624-23090-HZ2xWl9tZlzbiVvJMwM6ig],[server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 8 Mar 2010 15:25:58 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-x-gmail.com] Dear Taye, Would be nice to know what the fate of the H2 was, and to know more about the 2 C atoms that separated ... John McKelvey - Show quoted text - On Mon, Mar 8, 2010 at 10:00 AM, Taye Beyene D sene3095]-[yahoo.com wrote: > > Sent to CCL by: "Taye Beyene D" [sene3095*|*yahoo.com] > Hi all, I have built fullerene C60 molecule and I have the cartesian coor= dinates. But my major aim is to put hydrogen molecule inside the fullerene = molecule. When I put it inside the fullerene oppens by removing two carbons= from the cage. If you have some solutions please send me an advice. Thank = you in advance. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel _ gmail.com On Mon, Mar 8, 2010 at 10:00 AM, Taye Beyene D sene3095]-[yahoo.com wrote: > > Sent to CCL by: "Taye Beyene D" [sene3095*|*yahoo.com] > Hi all, I have built fullerene C60 molecule and I have the cartesian coor= dinates. But my major aim is to put hydrogen molecule inside the fullerene = molecule. When I put it inside the fullerene oppens by removing two carbons= from the cage. If you have some solutions please send me an advice. Thank = you in advance. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel _ gmail.com From owner-chemistry@ccl.net Mon Mar 8 16:04:00 2010 From: "David Gallagher gallagher.da,gmail.com" To: CCL Subject: CCL: Turbomole Training, March 2010 - Update Message-Id: <-41390-100308134820-31460-2shA/bRsWCgR6UiiMBhDUg*o*server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="=====================_1887421==.ALT" Date: Mon, 08 Mar 2010 10:20:12 -0800 Mime-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da-$-gmail.com] --=====================_1887421==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Turbomole (quantum chemistry) Training, 23rd March 2010 at ACS Update The Turbomole introductory training course will be held at 4.30 PM - 6.00PM on Tuesday 23rd March 2010 in Room 110, Moscone Center, San Francisco (during ACS), after the User Group Meeting. New users and anyone interested to learn more about Turbomole are welcome to register with for this free training session. A copy of Turbomole will be provided, but please bring your own laptop. Further information is posted at http://cacheresearch.com/aiche.html#training . --=====================_1887421==.ALT Content-Type: text/html; charset="us-ascii" Turbomole (quantum chemistry) Training, 23rd March 2010 at ACS

Update
The Turbomole introductory training course will be held at 4.30 PM - 6.00PM on Tuesday 23rd March 2010 in Room 110, Moscone Center, San Francisco (during ACS), after the User Group Meeting.  New users and anyone interested to learn more about Turbomole are welcome to register with <dgallagher(~)CACheResearch.com> for this free training session.  A copy of Turbomole will be provided, but please bring your own laptop. 

Further information is posted at http://cacheresearch.com/aiche.html#training .
--=====================_1887421==.ALT-- From owner-chemistry@ccl.net Mon Mar 8 23:05:00 2010 From: "Joaquin Barroso Flores joaco_barroso..yahoo.com" To: CCL Subject: CCL: interpretation the Natural Bond Orbitals (NBO) results Message-Id: <-41391-100308213308-11248-NXACPGNVAmxstGhXBYAG3w###server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-730399158-1268098372=:81654" Date: Mon, 8 Mar 2010 17:32:52 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso(!)yahoo.com] --0-730399158-1268098372=:81654 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear May=0A=0APlease let me refer to you to my blog where you can find the = information you are requesting. I suggest you visit the references section= =C2=A0listed within the same post for further info. At the same time I woul= d like to encourage you to do some previous search on the internet=C2=A0bef= ore posting=C2=A0questions to the ccl.=0A=0Ahttp://joaquinbarroso.wordpress= .com/2009/11/11/nbo/=0A=C2=A0=0AHope its helps=0A=0AJoaqu=C3=ADn=0A=C2=A0= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=0AJoaquin Barroso-Flores, Ph. D.=0AFacultatea de Chimie, Universitat= ea Babes-Bolyai=0ACluj-Napoca, Romania =0A=0A=0A-> http://joaquinbarroso.co= m=0A-> http://joaquinbarroso.wordpress.com=0A=0A=0Ajoaquinbarroso''a''chem.= ubbcluj.ro=0Ajoaquin.barroso''a''gmail.com =0A=0A=0A"Blogastronom=C3=ADa": = http://joaquinbarroso.blogspot.com =0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =0A=0A=0A=0A=0A______________= __________________=0ADe: may abdelghani may01dz##yahoo.fr =0APara: "Flores, Joaquin Barroso " =0AEnviado: s=C3=A1bado, 6 de marzo, 2010 4:08:55=0AAsunto: CCL: interpre= tation the Natural Bond Orbitals (NBO) results=0A=0A=0ADear CCL'ers=0A>1. W= hat we mean by the world "antibond BD*" in the output of NBO; or I have in = my NBO output the flowing sentences:=0A>575. (0.66522) BD ( 1)Ru 3-Ru 4=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=0A>=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0(=C2=A0=C2=A04.23%)= =C2=A0=C2=A0=C2=A00.2056*Ru 3 s( 76.43%)p 0.04(=C2=A0=C2=A02.89%)d 0.27( 20= .69%)=0A>576. (0.47855) BD*( 1)Ru 3-Ru 4=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=0A>= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0( 95.77%)=C2=A0=C2=A0=C2=A00.9786*Ru 3 s( 76.43%)p 0.0= 4(=C2=A0=C2=A02.89%)d 0.27( 20.69%)=0A>The question is: I have a bond betwe= en the atom Ru3 and Ru4 or not=E2=80=A6what is the bonding character of thi= s bond?=0A>=0A>=0A>2. There is any relationship between the =C2=ABcluster v= alence electron" concept and the results of =C2=ABNatural Electron Configur= ation"?=0A>=0A>=0A>=0A>4. In terms of single, double and triple bonds, wher= e=C2=A0=C2=A0we classify that of=C2=A0=C2=A0non-Lewis-type NBOs=C2=A0=C2=A0= : BD*, RY* and LP?=0A>=0A>=0A>5. Can the version 3 of NBO software, NBO.3, = give a=C2=A0credibility=C2=A0description of metal-metal bond?=0A>thank a lo= t for all,=0A>=0A> =0A=0A=0A=0A Encuentra las mejores recetas en Yahoo= ! Cocina. =0Ahttp://mx.mujer.yahoo.com/cocina/ --0-730399158-1268098372=:81654 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
=0A
Dear May
=0A
 
=0APlease let me refer to you to my blog where you can find the information = you are requesting. I suggest you visit the references section listed = within the same post for further info. At the same time I would like to enc= ourage you to do some previous search on the internet before posting&n= bsp;questions to the ccl.
=0A
 
=0A=0A
 
=0AHope its helps=0A
 
=0A
Joaqu=C3=ADn
 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D
Joaquin Barroso-Flores, Ph. D.
Facultatea de Chimie, Uni= versitatea Babes-Bolyai
Cluj-Napoca, Romania =0A


=0A-> http://joaquinbarroso.com
-> http://joaquinbarroso.wordpress= .com


=0A
joaquinbarroso''a''chem.ubbcluj.ro
joaquin.bar= roso''a''gmail.com


=0A
"Blogastronom=C3=ADa": http://joaq= uinbarroso.blogspot.com
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =0A

=0A

=0A=
=0A
=0ADe: may abdelghani may01dz##yahoo.fr <own= er-chemistry _ ccl.net>
Para: "Flores, Joaquin Barroso " <joaco_barroso _ yahoo.com>Enviado: s=C3=A1bado, 6 d= e marzo, 2010 4:08:55
Asunto: CCL: interpretation the Natural Bond Orbitals (NBO) results

=0A=0A=0A= =0A
=0A
=0A
=0A=
=0A

Dear CCL'ers

=0A

1. What we mean by the wor= ld "antibond BD*" in the output of NBO; or I have in my NBO output the flow= ing sentences:

=0A

575. (0.66522) BD ( 1)Ru 3-Ru 4     

=0A

           &= nbsp;    (  4.23%)   0.2056*Ru 3 s( 76.43%)p 0.= 04(  2.89%)d 0.27( 20.69%)

=0A

576. (0.47855) BD*( 1)Ru 3-R= u 4  &nbs= p;  

=0A

        &n= bsp;       ( 95.77%)   0.978= 6*Ru 3 s( 76.43%)p 0.04(  2.89%)d 0.27( 20.69%)

=0A

The question i= s: I have a bond between the atom Ru3 and Ru4 or not=E2=80=A6what is the bo= nding character of this bond?

=0A


=0A

2. There is any relationship b= etween the =C2=ABcluster valence electron" concept and the results of =C2= =ABNatural Electron Configuration"?

=0A


=0A

4. In terms of single, double and triple bonds, where = ; we cl= assify that of  non-Lewis-type NBOs&= nbsp; : BD*, RY* and LP?

=0A


=0A

5. Can the version 3 of NBO software, NBO.3, give a credibility description of metal-metal b= ond?

=0A

thank a lot for all,

=0A



<= /div>
=0A=0A=0A=0A

=C2=A1Encuentra las mejores recetas
con Yahoo! Cocina!
=0Ahttp://= mx.mujer.yahoo.com/cocina/ --0-730399158-1268098372=:81654--