From owner-chemistry@ccl.net Thu Nov 7 07:34:00 2013 From: "Olasunkanmi Lukman Olawale walecomuk%%yahoo.co.uk" To: CCL Subject: CCL: NBO calculation Message-Id: <-49311-131107072456-20776-XhkwBJnMfZZXHxBnRJjVlA ~ server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="1670751155-1111470332-1383827089=:21561" Date: Thu, 7 Nov 2013 12:24:49 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk|-|yahoo.co.uk] --1670751155-1111470332-1383827089=:21561 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Partha,=0AMetal complexation at a group close to N - H in your molecule = may lead to an increase in N-H bond length, this is not something unexpecte= d. But an increase in electron-occupancy at N-H is sort of contrary. Perhap= s you may want to check bond orders of N-H bond before and after complexati= on. This should give you a better idea of what happened.=0ABest regards.=0A= =0A=0A=C2=A0=0AOlasunkanmi Lukman Olawale=0A=0A____________________________= ____=0ACurrent Address:=0ADepartment of Chemistry,=0AObafemi Awolowo Univer= sity,=0AIle-Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-52401564 Or +234-0-8= 0-67161091=0A________________________________=0A =0A=0A=0A=0AOn Wednesday, = 6 November 2013, 17:29, Jean-Pierre DJUKIC djukic:-:unistra.fr wrote:=0A =0A=0ASent to CCL by: Jean-Pierre DJUKIC [djukic-x-= unistra.fr]=0ADear Partha,=0A=0AWhat is your functional that served to opti= mize your geometry ? are you =0Acomparing a range of cmpds modeled with the= same functional/basis set ?=0A=0AHow does the N-H bond relate to the metal= ? remote interaction ?=0A=0Ahave you checked the natural charge variation = of your ligand upon =0A"metalation"?=0A=0AYou ask too many questions and gi= ve few details, it is difficult to answer.=0A=0ABest regards,=0A=0AJP=0A=0A= Le 06/11/2013 10:45, partha kundu partha1kundu_-_gmail.com a =C3=A9crit := =0A> Dear All,=0A> I have done NBO calculation of some molecule. It is show= ing the e-=0A> occupancy of N-H bond to increase after some metal binding a= t some other=0A> group close to it. However the bond length of N-H has seen= to increase=0A> which is counterintuitive. Similar trend I found for C-N b= onds too.How=0A> can I explain this? What are the other things I need to lo= ok for?=0A> Thanks in advance.=0A>=0A> Partha=0A=0A-- =0A++++++++++++++++++= ++++++++++++++++++++++++++++++++++++++++++++++++=0ADr Jean-Pierre DJUKIC (= =C4=90uki=C4=87)=0A(DR CNRS)=0AAdresse postale:=0AInstitut de Chimie de Str= asbourg=0AUMR 7177 CNRS / Universit=C3=A9 de Strasbourg=0A4, rue Blaise Pas= cal=0A67000 Strasbourg Cedex.=0A=0Ame joindre: Institut Le bel, aile nord, = 9=C3=A8me =C3=A9tage, pi=C3=A8ce 942b, tel: +33 =0A(0)368851523=0A=0A++++++= ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=0AConseiller s= cientifique de l'Universit=C3=A9 de Strasbourg , secteur 2=0A=0Ahttp://www.= researcherid.com/rid/E-1262-2013=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=0Aa.k.a. F4HCV=0A=0A=0A=0A-=3D This is automatically added to eac= h message by the mailing script =3D-=0ATo recover the email address of the = author of the message, please change=0Athe strange characters on the top li= ne to the !=! sign. You can also=0Alook up the X-Original-From: line in the m= ail header.=0A=0A=0A=C2=A0 = =C2=A0 =C2=A0=0A=0AE-mail t= o administrators: CHEMISTRY-REQUEST!=!ccl.net or use=0A=C2=A0 =C2=A0 =C2=A0 h= ttp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0A= =0A=C2=A0 =C2=A0 =C2=A0=0A=0AB= efore posting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.= ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/announcements/= conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/i= ndex.shtml=0A=0A=0A= =C2=A0 =C2=A0 =C2=A0=0A=0ARTFI: http://www.= ccl.net/chemistry/aboutccl/instructions/ --1670751155-1111470332-1383827089=:21561 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Partha,
Metal complexation at a group close to N - H in= your molecule may lead to an increase in N-H bond length, this is not some= thing unexpected. But an increase in electron-occupancy at N-H is sort of c= ontrary. Perhaps you may want to check bond orders of N-H bond before and a= fter complexation. This should give you a better idea of what happened.
= Best regards.

 
Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
=
+234-0-80-52401564 Or +23= 4-0-80-67161091



On Wednesday, 6 November 2013, 17:29, Jea= n-Pierre DJUKIC djukic:-:unistra.fr <owner-chemistry!=!ccl.net> wrote:<= br>

Sent to CCL by: Jean= -Pierre DJUKIC [djukic-x-unistra.fr]
Dear Partha,

What is your fu= nctional that served to optimize your geometry ? are you
comparing a ra= nge of cmpds modeled with the same functional/basis set ?

How does t= he N-H bond relate to the metal ? remote interaction ?

have you chec= ked the natural charge variation of your ligand upon
"metalation"?
<= br>You ask too many questions and give few details, it is difficult to answ= er.

Best regards,

JP

Le 06/11/2013 10:45, partha kundu= partha1kundu_-_gmail.com a =C3=A9crit :
> Dear All,
> I have d= one NBO calculation of some molecule. It is showing the e-
> occupanc= y of N-H bond to increase after some metal binding at some other
> gr= oup close to it. However the bond length of N-H has seen to increase
> w= hich is counterintuitive. Similar trend I found for C-N bonds too.How
&g= t; can I explain this? What are the other things I need to look for?
>= ; Thanks in advance.
>
> Partha

--
+++++++++++++++++= +++++++++++++++++++++++++++++++++++++++++++++++++
Dr Jean-Pierre DJUKIC = (=C4=90uki=C4=87)
(DR CNRS)
Adresse postale:
Institut de Chimie de= Strasbourg
UMR 7177 CNRS / Universit=C3=A9 de Strasbourg
4, rue Blai= se Pascal
67000 Strasbourg Cedex.

me joindre: Institut Le bel, ai= le nord, 9=C3=A8me =C3=A9tage, pi=C3=A8ce 942b, tel: +33
(0)368851523
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++Conseiller scientifique de l'Universit=C3=A9 de Strasbourg , secteur 2
=
http://www.researcherid.com/rid/E-1262-2013
=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
a.k.a. F4HCV


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--1670751155-1111470332-1383827089=:21561-- From owner-chemistry@ccl.net Thu Nov 7 11:43:00 2013 From: "Douglas B. Staple dstaple..dal.ca" To: CCL Subject: CCL:G: SCF convergence failure with AUG-cc-pVDZ basis in Gaussian 09 Message-Id: <-49312-131107102444-14862-9iQ6bxCvAiUmby904AEr1w-x-server.ccl.net> X-Original-From: "Douglas B. Staple" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 07 Nov 2013 11:23:56 -0400 MIME-Version: 1.0 Sent to CCL by: "Douglas B. Staple" [dstaple- -dal.ca] I received several good suggestions from various people: 1) S. Lehtola suggested deleting the diffuse functions from the hydrogens. 2) S. Lehtola also suggested SCF=XQC, and trying Jensen's basis sets. 3) K. Peterson suggested removing the diffuse s function for each atom. 4) H. A. J. Vazquez suggested SCF(NoVarAcc,NoIncFock,TIGHT) 5) V. Chaban suggested decreasing SCF requirements, e.g. SCF=Conver=7 I should say right away that the calculation converged fine with SCF(NoVarAcc,NoIncFock,Tight). To me, this is a bit of black magic. From reading the Gaussian 09 manual, I thought that NoIncFock and Tight were the defaults, but deleting them causes convergence to fail. So I'm not sure yet which of these keywords are necessary for convergence or why. Nevertheless, thank you very much for getting my calculation to converge! Reducing the number of diffuse functions as suggested by S. Lehtola and K. Peterson seems like a very logical and good idea. Unfortunately the version of Gaussian 09 I have (Revision C.01) doesn't have the calendar basis functions, and I honestly don't know how to reduce the number of diffuse functions in AUG-cc-pVDZ any other way. I'm looking into getting access to g09 Rev. D, which has the calendar basis sets. The job with SCF=XQC failed to converge; the error message was: Linear equations converged to 1.646D-10 1.646D-09 after 31 iterations. Density matrix breaks symmetry, PCut= 1.47D-04 Rerun with SCF=IntRep. I didn't try rerunning with SCF(XQC,IntRep), because I'd previously tried the QC-version of that to no avail. The job with SCF=Conver=7 failed to converge; the error message was "Convergence failure -- run terminated." as before. Thank you all very much for your help! Doug Staple dstaple++dal.ca From owner-chemistry@ccl.net Thu Nov 7 12:17:00 2013 From: "partha kundu partha1kundu . gmail.com" To: CCL Subject: CCL: NBO calculation Message-Id: <-49313-131107115012-17535-F7JWvtaVvBygSrJ0Tcblwg|-|server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary=485b3970cc72bf8ded04ea990e10 Date: Thu, 7 Nov 2013 22:19:25 +0530 MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu^^gmail.com] --485b3970cc72bf8ded04ea990e10 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Dr. Olawale, Thanks for your response. Actually I did some mistake in assigning the overall charge of the molecule. Now after adding proper charge the N-H problem has been solved. But I still have problem with C-N bond where electron occupancy is decreased, but the bond distance also has decreased. So according to you the electron occupancy alone cannot decide the distance of bond and needs to calculate bond order? Actually I have G09 B.01 version which cannot compute bond order. Is there any other way to tackle this problem? Thanks and regards. Partha. On Thu, Nov 7, 2013 at 5:54 PM, Olasunkanmi Lukman Olawale walecomuk%% yahoo.co.uk wrote: > Hi Partha, > Metal complexation at a group close to N - H in your molecule may lead to > an increase in N-H bond length, this is not something unexpected. But an > increase in electron-occupancy at N-H is sort of contrary. Perhaps you ma= y > want to check bond orders of N-H bond before and after complexation. This > should give you a better idea of what happened. > Best regards. > > > Olasunkanmi Lukman Olawale > ------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------ > > > On Wednesday, 6 November 2013, 17:29, Jean-Pierre DJUKIC djukic:-: > unistra.fr wrote: > > Sent to CCL by: Jean-Pierre DJUKIC [djukic-x-unistra.fr] > Dear Partha, > > What is your functional that served to optimize your geometry ? are you > comparing a range of cmpds modeled with the same functional/basis set ? > > How does the N-H bond relate to the metal ? remote interaction ? > > have you checked the natural charge variation of your ligand upon > "metalation"? > > You ask too many questions and give few details, it is difficult to > answer. > > Best regards, > > JP > > Le 06/11/2013 10:45, partha kundu partha1kundu_-_gmail.com a =C3=A9crit : > > Dear All, > > I have done NBO calculation of some molecule. It is showing the e- > > occupancy of N-H bond to increase after some metal binding at some othe= r > > group close to it. However the bond length of N-H has seen to increase > > which is counterintuitive. Similar trend I found for C-N bonds too.How > > can I explain this? What are the other things I need to look for? > > Thanks in advance. > > > > Partha > > -- > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Dr Jean-Pierre DJUKIC (=C4=90uki=C4=87) > (DR CNRS) > Adresse postale: > Institut de Chimie de Strasbourg > UMR 7177 CNRS / Universit=C3=A9 de Strasbourg > 4, rue Blaise Pascal > 67000 Strasbourg Cedex. > > me joindre: Institut Le bel, aile nord, 9=C3=A8me =C3=A9tage, pi=C3=A8ce = 942b, tel: +33 > (0)368851523 > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Conseiller scientifique de l'Universit=C3=A9 de Strasbourg , secteur 2 > > http://www.researcherid.com/rid/E-1262-2013 > =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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > a.k.a. F4HCV > > > > -=3D This is automatically added to each message by the mailing script = =3D-> E-mail to subscribers: CHEMISTRY#%#ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST#%#ccl.net or use> > > > > --485b3970cc72bf8ded04ea990e10 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Dr. Olawale,
Thanks = for your response. Actually I did some mistake in assigning the overall cha= rge of the molecule. Now=C2=A0 after adding proper charge the N-H problem h= as been solved. But I still have problem with C-N bond where electron occup= ancy is decreased, but the bond distance also has decreased. So according t= o you the electron occupancy alone cannot decide the distance of bond and n= eeds to calculate bond order? Actually I=C2=A0 have G09 B.01 version which = cannot compute bond order. Is there any other way to tackle this problem?
Thanks and regards.

Partha.


On Thu, Nov 7, 2013 at 5:54 PM, Olasunka= nmi Lukman Olawale walecomuk%%yahoo.co.uk <owner-chemistry_-_ccl.net> wrote:
Hi= Partha,
Metal complexation at a group close to N - H in your molecule= may lead to an increase in N-H bond length, this is not something unexpect= ed. But an increase in electron-occupancy at N-H is sort of contrary. Perha= ps you may want to check bond orders of N-H bond before and after co= mplexation. This should give you a better idea of what happened.
Best regards.

=C2=A0
Olasunkanmi Lukma= n Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo Univers= ity,
Ile-Ife, Osun State.
Nigeria.
+234-0-80-52401564 Or +234-0-80-67161091



On Wednesday, 6 November 2013, 17:29, Jean-Pierre DJ= UKIC djukic:-:unistra.fr<= /span> <owner-chemistry#%#ccl.net> wrote:

Sent to CCL by: Jean-Pierre DJUKIC [djukic-x-u= nistra.fr]
Dear Partha,

What is your functional that served to optimize your ge= ometry ? are you
comparing a range of cmpds modeled with the same functional/basis set ?

How does the N-H bond relate to the metal ? remote intera= ction ?

have you checked the natural charge variation = of your ligand upon
"metalation"?

You ask too many questions and= give few details, it is difficult to answer.

Best regards,

JP

Le 06/11/2013 10:45, partha
kundu partha1kundu_-_gmail.com a =C3=A9crit :
> Dear All,
> I have done NBO calculation of some molecule. It is = showing the e-
> occupancy of N-H bond to increase afte= r some metal binding at some other
> group close to it. However the bond length of N-H has seen to incr= ease
> which is counterintuitive. Similar trend I found= for C-N bonds too.How
> can I explain this? What are the other things I need to = look for?
> Thanks in advance.
>
> Partha

--
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr Jean-Pierre DJUKIC (=C4=90uki=C4=87)
(DR CNRS)
Adresse postale:
Institut de Chimie de Strasbourg
UMR 7177 CNRS / Universit=C3=A9 de Stra= sbourg
4, rue Blaise Pascal
67000 Strasbourg Cedex.

me joindre= : Institut Le bel, aile nord, 9=C3=A8me =C3=A9tage, pi=C3=A8ce 942b, tel: += 33
(0)368851523

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
C= onseiller scientifique de l'Universit=C3=A9 de Strasbourg , secteur 2
http://www.researcherid.com/rid/E-1262-2013
=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
a.k.a. F4= HCV



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--485b3970cc72bf8ded04ea990e10-- From owner-chemistry@ccl.net Thu Nov 7 13:34:00 2013 From: "Susi Lehtola susi.lehtola(_)alumni.helsinki.fi" To: CCL Subject: CCL:G: SCF convergence failure with AUG-cc-pVDZ basis in Gaussian 09 Message-Id: <-49314-131107131627-12277-njxQlyXgkExmTJLOxkWSyw:-:server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 7 Nov 2013 20:16:14 +0200 Mime-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola- -alumni.helsinki.fi] On Thu, 07 Nov 2013 11:23:56 -0400 "Douglas B. Staple dstaple..dal.ca" wrote: > 3) K. Peterson suggested removing the diffuse s function for each atom. Kirk's suggestion would have probably solved the problem (as your calculations converged fine with the non-augmented basis sets), but removing *all* the diffuse s functions is a rather drastic procedure. > 4) H. A. J. Vazquez suggested SCF(NoVarAcc,NoIncFock,TIGHT) > 5) V. Chaban suggested decreasing SCF requirements, e.g. SCF=Conver=7 > > I should say right away that the calculation converged fine with > SCF(NoVarAcc,NoIncFock,Tight). To me, this is a bit of black magic. From > reading the Gaussian 09 manual, I thought that NoIncFock and Tight were > the defaults, but deleting them causes convergence to fail. So I'm not > sure yet which of these keywords are necessary for convergence or why. > Nevertheless, thank you very much for getting my calculation to converge! > From what I gather from the Gaussian manual, SCF=Tight is the default, and so are VarAcc and IncFock. Because VarAcc only affects the initial steps of the SCF cycle, it shouldn't be a problem. I believe the problems were caused by IncFock, which here refers to incremental formation of the Coulomb matrix. Since this is linear in the density matrix J(uv) = sum_{rs} (uv|rs) P(rs) you don't have to recompute all contributions every cycle, but just calculate the contribution from the last cycle dJ(uv) = sum_{rs} (uv|rs) dP(rs) Although this can speed up the calculation, it also can lead to creep of numerical errors: although the change in density can be small for a couple of iteration, the small changes can accumulate into something that is large. Also, it occurred to me that you are not using density fitting (a.k.a. RI-J). If you use pure DFT functionals (e.g. PBEPBE and BP86), enabling density fitting usually speeds up the calculation quite a bit. Also, AFAIK incremental formation is not usually performed in RI-J, since the integrals are much faster to compute anyway, so you might not need the NoIncFock keyword. To do RI-J just change #P PBEPBE/aug-cc-pVDZ to #P PBEPBE/aug-cc-pVDZ/Auto which will use an automatically generated fitting basis set. > Reducing the number of diffuse functions as suggested by S. Lehtola and > K. Peterson seems like a very logical and good idea. Unfortunately the > version of Gaussian 09 I have (Revision C.01) doesn't have the calendar > basis functions, and I honestly don't know how to reduce the number of > diffuse functions in AUG-cc-pVDZ any other way. I'm looking into > getting access to g09 Rev. D, which has the calendar basis sets. You can always define the basis set to use by hand. Unfortunately the calendar basis sets aren't currently available at the Basis Set Exchange.. -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Postdoctoral researcher susi.lehtola[*]alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola[*]alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto --------------------------------------------------------------- From owner-chemistry@ccl.net Thu Nov 7 14:23:00 2013 From: "JP DJUKIC djukic~!~unistra.fr" To: CCL Subject: CCL: NBO calculation Message-Id: <-49315-131107134426-25549-QtKyvBRBcANIkg63+rkrjA|-|server.ccl.net> X-Original-From: JP DJUKIC Content-Type: multipart/alternative; boundary="------------080805030505020005040603" Date: Thu, 07 Nov 2013 19:43:58 +0100 MIME-Version: 1.0 Sent to CCL by: JP DJUKIC [djukic^unistra.fr] This is a multi-part message in MIME format. --------------080805030505020005040603 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Dear Partha; Wiberg bond index determination is possible within GENNBO, it is a basic calculation that is generally performed in the default setting. You should read the NBO manual carefully. What kind of C atom is bonded to your N atom ? Regards, JP Le 07/11/2013 17:49, partha kundu partha1kundu . gmail.com a écrit : > Dear Dr. Olawale, > Thanks for your response. Actually I did some mistake in assigning the > overall charge of the molecule. Now after adding proper charge the > N-H problem has been solved. But I still have problem with C-N bond > where electron occupancy is decreased, but the bond distance also has > decreased. So according to you the electron occupancy alone cannot > decide the distance of bond and needs to calculate bond order? > Actually I have G09 B.01 version which cannot compute bond order. Is > there any other way to tackle this problem? > Thanks and regards. > > Partha. > > > On Thu, Nov 7, 2013 at 5:54 PM, Olasunkanmi Lukman Olawale > walecomuk%%yahoo.co.uk > wrote: > > Hi Partha, > Metal complexation at a group close to N - H in your molecule may > lead to an increase in N-H bond length, this is not something > unexpected. But an increase in electron-occupancy at N-H is sort > of contrary. Perhaps you may want to check bond orders of N-H bond > before and after complexation. This should give you a better idea > of what happened. > Best regards. > > Olasunkanmi Lukman Olawale > ------------------------------------------------------------------------ > Current Address: > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Osun State. > Nigeria. > +234-0-80-52401564 Or +234-0-80-67161091 > ------------------------------------------------------------------------ > > > On Wednesday, 6 November 2013, 17:29, Jean-Pierre DJUKIC > djukic:-:unistra.fr > wrote: > > Sent to CCL by: Jean-Pierre DJUKIC [djukic-x-unistra.fr > ] > Dear Partha, > > What is your functional that served to optimize your geometry ? > are you > comparing a range of cmpds modeled with the same functional/basis > set ? > > How does the N-H bond relate to the metal ? remote interaction ? > > have you checked the natural charge variation of your ligand upon > "metalation"? > > You ask too many questions and give few details, it is difficult > to answer. > > Best regards, > > JP > > Le 06/11/2013 10:45, partha kundu partha1kundu_-_gmail.com > a écrit : > > Dear All, > > I have done NBO calculation of some molecule. It is showing the e- > > occupancy of N-H bond to increase after some metal binding at > some other > > group close to it. However the bond length of N-H has seen to > increase > > which is counterintuitive. Similar trend I found for C-N bonds > too.How > > can I explain this? What are the other things I need to look for? > > Thanks in advance. > > > > Partha > > -- > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Dr Jean-Pierre DJUKIC (Đukić) > (DR CNRS) > Adresse postale: > Institut de Chimie de Strasbourg > UMR 7177 CNRS / Université de Strasbourg > 4, rue Blaise Pascal > 67000 Strasbourg Cedex. > > me joindre: Institut Le bel, aile nord, 9ème étage, pièce 942b, > tel: +33 > (0)368851523 > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > Conseiller scientifique de l'Université de Strasbourg , secteur 2 > > http://www.researcherid.com/rid/E-1262-2013 > ================================================================== > a.k.a. F4HCV > > > > -= This is automatically added to each message by the mailing > script =- > 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/> > > > > --------------080805030505020005040603 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit
Dear Partha;

Wiberg bond index determination is possible within GENNBO, it is a basic calculation that is generally performed in the default setting.

You should read the NBO manual carefully.

What kind of C atom is bonded to your N atom ?

Regards,

JP
Le 07/11/2013 17:49, partha kundu partha1kundu . gmail.com a écrit :
Dear Dr. Olawale,
Thanks for your response. Actually I did some mistake in assigning the overall charge of the molecule. Now  after adding proper charge the N-H problem has been solved. But I still have problem with C-N bond where electron occupancy is decreased, but the bond distance also has decreased. So according to you the electron occupancy alone cannot decide the distance of bond and needs to calculate bond order? Actually I  have G09 B.01 version which cannot compute bond order. Is there any other way to tackle this problem?
Thanks and regards.

Partha.


On Thu, Nov 7, 2013 at 5:54 PM, Olasunkanmi Lukman Olawale walecomuk%%yahoo.co.uk <owner-chemistry##ccl.net> wrote:
Hi Partha,
Metal complexation at a group close to N - H in your molecule may lead to an increase in N-H bond length, this is not something unexpected. But an increase in electron-occupancy at N-H is sort of contrary. Perhaps you may want to check bond orders of N-H bond before and after complexation. This should give you a better idea of what happened.
Best regards.

 
Olasunkanmi Lukman Olawale

Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.
+234-0-80-52401564 Or +234-0-80-67161091



On Wednesday, 6 November 2013, 17:29, Jean-Pierre DJUKIC djukic:-:unistra.fr <owner-chemistry#%#ccl.net> wrote:

Sent to CCL by: Jean-Pierre DJUKIC [djukic-x-unistra.fr]
Dear Partha,

What is your functional that served to optimize your geometry ? are you
comparing a range of cmpds modeled with the same functional/basis set ?

How does the N-H bond relate to the metal ? remote interaction ?

have you checked the natural charge variation of your ligand upon
"metalation"?

You ask too many questions and give few details, it is difficult to answer.

Best regards,

JP

Le 06/11/2013 10:45, partha kundu partha1kundu_-_gmail.com a écrit :
> Dear All,
> I have done NBO calculation of some molecule. It is showing the e-
> occupancy of N-H bond to increase after some metal binding at some other
> group close to it. However the bond length of N-H has seen to increase
> which is counterintuitive. Similar trend I found for C-N bonds too.How
> can I explain this? What are the other things I need to look for?
> Thanks in advance.
>
> Partha

--
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr Jean-Pierre DJUKIC (Đukić)
(DR CNRS)
Adresse postale:
Institut de Chimie de Strasbourg
UMR 7177 CNRS / Université de Strasbourg
4, rue Blaise Pascal
67000 Strasbourg Cedex.

me joindre: Institut Le bel, aile nord, 9ème étage, pièce 942b, tel: +33
(0)368851523

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Conseiller scientifique de l'Université de Strasbourg , secteur 2

http://www.researcherid.com/rid/E-1262-2013
==================================================================
a.k.a. F4HCV



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--------------080805030505020005040603-- From owner-chemistry@ccl.net Thu Nov 7 18:06:01 2013 From: "=?iso-8859-1?Q?Hugo_Alejandro_Jim=E9nez_V=E1zquez?= hjimenez!=!woodward.encb.ipn.mx" To: CCL Subject: CCL:G: SCF convergence failure with AUG-cc-pVDZ basis in Gaussian 09 Message-Id: <-49316-131107173518-8288-y5b7V/ULBD9myz8aGrzN/g_-_server.ccl.net> X-Original-From: =?iso-8859-1?Q?Hugo_Alejandro_Jim=E9nez_V=E1zquez?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 7 Nov 2013 16:34:21 -0600 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Hugo_Alejandro_Jim=E9nez_V=E1zquez?= [hjimenez**woodward.encb.ipn.mx] The use of "NoVarAcc" and "NoIncFock" was suggested by G W Trucks from Gaussian Inc after I asked for help because I had serious convergence problems with the aug-CC-pVTZ basis set. He actually sent me an extensive account of recommendations for dealing with these problems. I am including his message below as it might be useful to others. In the past "Tight" was not the default SCF option for single-point calculations. Even though it seems to be the default now, I always include it for all my single point calculations. Concerning the comment by Douglas of not being able to use the calendar basis sets in previous revisions of Gaussian, I can tell you that you can do it by hand. You can "print" the full aug-CC-pVDZ or aug-CC-pVTZ basis sets and remove the diffuse functions you do not want by hand. I made calculations in this way with G09 Rev B.01 at the MP2/maug-CC-pVTZ level of theory, using the description of the basis set given in JCTC 2009, 5 1197 as a guide for the functions that had to be removed. Once I removed the diffuse functions I did not want, the modified basis set was read in by Gaussian with GEN. I know, it is a lot of work, but it works because you have to do it for each atom. Now I have Rev D.01, so I do not have to worry very much for this. By the way. I did not have any convergence problems with the maug-CC-pVTZ basis set. Hugo ----------------------------------------------------------------- Dr. Hugo A. Jimenez Vazquez, Before answering your specific questions below, many problems with SCF convergence and PCM are a result of a poor structure. We highly recommend optimizing the gas state prior to introducing PCM. If you have not done that, it is my first suggestion. SCF convergence issues are not tied to a given basis set; rather, they are a symptom of occupying the proper orbitals to obtain the single determinant that provides the lowest energy for a particular state (as required by the SCF procedure). Larger basis sets have more orbitals so this becomes a harder a small basis set to find the correct state then use the result as a guess for the larger basis. problem. Diffuse basis sets have a number of orbitals which are poor candidates for occupation as well. It is often best to use It is also important to make sure you have the lowest solution for a given state. In order to test if you have the lowest single determinant, you can run a calculation with: stable=opt That option will determine if the determinant is a local minimum; otherwise, it will re-optimize the wavefunction. Even with a good starting guess at a particular geometry, if the initial structure is poor and changes drastically then one can expect the occupancy (order of the occupied orbitals) will also change. This means that the converged wavefunction for a previous step may provide a poor guess for the next step resulting in SCF convergence issues. Again, it emphasizes the need for a good starting structure. Assuming you checked the geometry, here are a few general guidelines to follow in cases of SCF convergence difficulties: 1) "SCF=NoVarAcc". This one requests the use of full integral accuracy from the first SCF cycle. The default is to use lower accuracy in the first few cycles in interest of speed and then switch to full accuracy as the SCF approaches convergence. In some cases, the initial lower integral accuracy is not good enough and the SCF procedure might do a lot of useless iterations. This option never hurts, it would make the first few cycles a little slower but the overall time may be lower if it takes fewer cycles to get close to convergence, so it is definitely the first thing to try. 2) Increase integral accuracy. The default thresholds are set for an integral accuracy of 10^-10. In some cases when using very diffuse functions, one might need to use tighter thresholds since there will be very small quantities being computed. The integral accuracy is controlled with "Integral=(Acc2E=N)" in G09 or by "IOp(5/87=N)" in G03. The default is N=10. One may try increasing the accuracy by one or two orders of magnitude (i.e. N=11 or N=12). 3) Tighten the grid for numerical integration in DFT (This does not apply to non-DFT jobs such as HF, MP2, etc.). The default ("Fine") grid for numerical integration is adequate for most purposes but in some cases the small numerical noise might make difficult SCF convergence and the SCF procedure takes too many iterations when it is close to convergence. If the problem is with large oscillations in early SCF cycles, this is likely not going to help. One can tighten the grid with "Integral=(Grid=XXXXX)", where XXXXX is the value of the integration grid (see the documentation of the "Integral" keyword for more details). In most cases, tightening the grid to the "Ultrafine" grid is sufficient. 4) "SCF=NoIncFock". Turning off the incremental Fock formation can help in cases with very diffuse functions. This increases the computational cost of the SCF calculation as it requests the recomputation of the full Fock matrix at each SCF cycle, instead of only doing an incremental Fock formation (default). There is an increase in the cost of the whole SCF procedure since the full Fock matrix is formed at every SCF cycle, but such increase in cost with respect to the default SCF procedure is lower than doing QC SCF. 5) "SCF=Fermi". This one does a combination of things including Fermi broadening, damping and level shifting, deciding dynamically the most suitable strategy. It can be helpful in cases with oscillations in early cycles of the SCF procedure, but I only recommend it in such cases and when the other options above do not make a difference on the early oscillations. 6) "SCF=XQC". Turns on the QC SCF procedure after the maximum number of regular SCF cycles have been done without convergence (if the SCF is converged in fewer cycles with the regular SCF procedure, then the QC step is skipped). The maximum number of regular SCF cycles by default is 128, and this can be controlled by "SCF=(MaxConventionalCyc=N)". The QC procedure is much slower than the regular SCF procedure but it is very robust and almost guaranteed to converge to an SCF solution. It also has higher chance to converge to the nearest SCF solution (which could be an unstable solution) than the regular SCF procedure, so it is strongly recommended to check for instabilities. The "SCF=XQC" option thus provides a fall-back solution when the regular SCF procedure fails to converge. As you see, the issue with SCF=XQC is that it will usually converge; however, it may well not be the desired one or the lowest. In the case of a compound method (like CBS), you have to worry about check the lowest solution is found in each step of the calculation. Often (and again not always), Gaussian will not change states with various methods except in cases where the potential energy surface differs significantly between the methods. Plotting the orbitals, checking the value of S**2 are recommended. If you continue to have problems, please send us a copy of your input (change .com to .gjf to avoid SPAM filters) and log files. Best regards, Gary W. Trucks, Ph.D. Gaussian, Inc. ----------------------------------------------------------------- -----Mensaje original----- > From: Susi Lehtola susi.lehtola(_)alumni.helsinki.fi Sent: Thursday, November 07, 2013 12:16 PM To: Jimnez-Vzquez, Hugo Alejandro Subject: CCL:G: SCF convergence failure with AUG-cc-pVDZ basis in Gaussian 09 Sent to CCL by: Susi Lehtola [susi.lehtola- -alumni.helsinki.fi] On Thu, 07 Nov 2013 11:23:56 -0400 "Douglas B. Staple dstaple..dal.ca" wrote: > 3) K. Peterson suggested removing the diffuse s function for each atom. Kirk's suggestion would have probably solved the problem (as your calculations converged fine with the non-augmented basis sets), but removing *all* the diffuse s functions is a rather drastic procedure. > 4) H. A. J. Vazquez suggested SCF(NoVarAcc,NoIncFock,TIGHT) > 5) V. Chaban suggested decreasing SCF requirements, e.g. SCF=Conver=7 > > I should say right away that the calculation converged fine with > SCF(NoVarAcc,NoIncFock,Tight). To me, this is a bit of black magic. From > reading the Gaussian 09 manual, I thought that NoIncFock and Tight were > the defaults, but deleting them causes convergence to fail. So I'm not > sure yet which of these keywords are necessary for convergence or why. > Nevertheless, thank you very much for getting my calculation to converge! > From what I gather from the Gaussian manual, SCF=Tight is the default, and so are VarAcc and IncFock. Because VarAcc only affects the initial steps of the SCF cycle, it shouldn't be a problem. I believe the problems were caused by IncFock, which here refers to incremental formation of the Coulomb matrix. Since this is linear in the density matrix J(uv) = sum_{rs} (uv|rs) P(rs) you don't have to recompute all contributions every cycle, but just calculate the contribution from the last cycle dJ(uv) = sum_{rs} (uv|rs) dP(rs) Although this can speed up the calculation, it also can lead to creep of numerical errors: although the change in density can be small for a couple of iteration, the small changes can accumulate into something that is large. Also, it occurred to me that you are not using density fitting (a.k.a. RI-J). If you use pure DFT functionals (e.g. PBEPBE and BP86), enabling density fitting usually speeds up the calculation quite a bit. Also, AFAIK incremental formation is not usually performed in RI-J, since the integrals are much faster to compute anyway, so you might not need the NoIncFock keyword. To do RI-J just change #P PBEPBE/aug-cc-pVDZ to #P PBEPBE/aug-cc-pVDZ/Auto which will use an automatically generated fitting basis set. > Reducing the number of diffuse functions as suggested by S. Lehtola and > K. Peterson seems like a very logical and good idea. Unfortunately the > version of Gaussian 09 I have (Revision C.01) doesn't have the calendar > basis functions, and I honestly don't know how to reduce the number of > diffuse functions in AUG-cc-pVDZ any other way. I'm looking into > getting access to g09 Rev. D, which has the calendar basis sets. You can always define the basis set to use by hand. Unfortunately the calendar basis sets aren't currently available at the Basis Set Exchange.. -- --------------------------------------------------------------- Mr. Susi Lehtola, PhD Postdoctoral researcher susi.lehtola_._alumni.helsinki.fi Department of Applied Physics http://www.helsinki.fi/~jzlehtol Aalto University Finland --------------------------------------------------------------- Susi Lehtola, FT Tutkijatohtori susi.lehtola_._alumni.helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Aalto-yliopisto ---------------------------------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt