From owner-chemistry@ccl.net Fri Dec 3 01:06:00 2010 From: "elsayed elmeselhy elsayed.elmes#%#yahoo.com" To: CCL Subject: CCL:G: Is the ferromagentic state = the triplet state? Message-Id: <-43266-101202220406-26554-V2kQgZIPXxkOc5ivzEB3lw,+,server.ccl.net> X-Original-From: elsayed elmeselhy Content-Type: multipart/alternative; boundary="0-1243833806-1291345030=:7674" Date: Thu, 2 Dec 2010 18:57:10 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: elsayed elmeselhy [elsayed.elmes_-_yahoo.com] --0-1243833806-1291345030=:7674 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dr. Adam, Many thanks for your clear answer. The best point you answered that the tri= plet state =3D ferromagentic state. However, my system is [Cu2L]4+, where t= he Cu...Cu distance is about 6 Ang. Then a carbonate anion reacts with it= =A0 forming bridge between the Cu-cations i.e. -Cu-CO3-Cu-.=A0=20 Regards, Sayed --- On Fri, 12/3/10, Johannes Johansson johjo76,gmail.com wrote: > From: Johannes Johansson johjo76,gmail.com Subject: CCL:G: Is the ferromagentic state =3D the triplet state? To: "Mesa, Sayed " Date: Friday, December 3, 2010, 2:03 AM Dear Sayed, I give my answers below. Sincerely / Johannes 2010/12/2 elsayed elmeselhy elsayed.elmes]-[yahoo.com =0ADear Dr. Adam, =0AThanks for your response. I would be appreciated if you clarified the fo= llowing points: 1- "A closed-shell singlet state of this system requires disproportionation= to a Cu(I)-Cu(III) oxidation state." =0A My system is [Cu2L]4+ where L is macrocyclic ligand. Both copper cations ha= ve oxidation state =3D +2. Could you explain me how and why the calculation= of a closed-shell singlet state of my system=A0 leads to disproportionatio= n to a Cu(I)-Cu(III) oxidation state. If there is a publication(s) refer to= that please, let me know. =0A I was a bit too fast here. Does your system have a direct Cu-Cu bond? If so= , then I guess a closed-shell singlet state is possible even if both ions a= re in oxidation states with odd number of electrons. (I was thinking about = systems in which there is no direct bond between the copper ions, e.g. Cu-O= -O-Cu, which can not have a closed-shell singlet state with zero spin on bo= th Cu-atoms if these are Cu(II) since it is an odd number ion (d9). In such= systems, the only possibility to get a closed-shell singlet state is if th= e Cu(II)/Cu(II) oxidation state disproportionates to Cu(I)/Cu(III), most li= kely a high energy state.)=0A Is there any experimental data available for your system? Maybe for a simil= ar system? Here is an exp ref for a bio-mimetic Cu(II)-O-O-Cu(II) complex, = which has an antiferromagnetic ground state:=A0Karlin et al, JACS, 1993, 11= 5, 2677. Karlin and co-workers have done a lot of exp work on Cu-dimers so = there might be more interesting papers for you in his work.=0A =A0=0A2- is the spin population ~1alfa on both Cu atoms in the triplet stat= e and =0A~1alfa and ~1beta on the Cu-atoms in the open-shell singlet state? =0A=A0=0ADid you mean to say open-shell triplet state=A0 (~1alfa on both Cu= atoms) and open-shell singlet state (~1alfa and ~1beta on the Cu-atoms), r= espectively?=20 =0A Yes (a triplet state is always open-shell). =0AIn the first case, there are two alpha for Cu2+, then it should be=A0 op= en shell triplet state: In other word, in the input file, we should fragmen= t=A0 the multiplicities of the molecule as the following: =0A3 :the=A0 multiplicity for whole complex (because the number of unpaired= eletrons =3D 2) 2 : the multiplicity for the first Cu(2+) (because the number of unpaired e= letrons =3D1) 2 : the multiplicity for the second Cu(2+) (because the number of unpaired = eletrons =3D 1) =0A1: the multiplicity for ligand (because the number of unpaired eletrons = =3D0) Yes, but to get the triplet state M=3D3 should be enough. To get the corres= ponding antiferromagnetic coupling, these specifications might be necessary= but then with M=3D1 for the system as a whole. (I have not done this with = Gaussian but is very easy with Jaguar or Turbomole.)=0A Good luck! / Johannes=A0=0APlease let me know your opinion=0A asap. Regards, Sayed --- On Thu, 12/2/10, Johannes Johansson johjo76..gmail.com wrote: =0A > From: Johannes Johansson johjo76..gmail.com =0ASubject: CCL: Is the ferromagentic state =3D the triplet state? To: "Mesa, Sayed " Date: Thursday, December 2, 2010, 5:23 PM=0A Dear Sayed, is the spin population ~1alfa on both Cu atoms in the triplet state and ~1a= lfa and ~1beta on the Cu-atoms in the open-shell singlet state? If so, then= these are the ferro- and antiferromagnetically coupled states respectively= . A closed-shell singlet state of this system requires disproportionation t= o a Cu(I)-Cu(III) oxidation state.=0A=0A Best regards / Johannes=A0 --=20 Adam Johannes Johansson Ph.D., M.Sc. Division of Physical Chemistry KTH (Royal Institute of Technology) Teknikringen 36 =0ASE-100 44 Stockholm Sweden Office: 087908217 =0ACell phone: 0708178487 E-mail:johjo76||gmail.com Research web page:www.physto.se/~johjo =0A=0A =0A=0A=0A=0A=0A=0A=0A=0A =20 --=20 Adam Johannes Johansson Ph.D., M.Sc. Division of Physical Chemistry KTH (Royal Institute of Technology) Teknikringen 36 SE-100 44 Stockholm Sweden =0AOffice: 087908217 Cell phone: 0708178487 E-mail:johjo76[-]gmail.com Research web page:www.physto.se/~johjo =0A=0A=0A=0A=0A --0-1243833806-1291345030=:7674 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dr. Adam,

Many thanks for your cl= ear answer. The best point you answered that the triplet state =3D ferromag= entic state. However, my system is [Cu2L]4+, where the Cu...Cu distance is = about 6 Ang. Then a carbonate anion reacts with it  forming bridge bet= ween the Cu-cations i.e. -Cu-CO3-Cu-. 

Regards,
Sayed
--- On Fri, 12/3/10, Johannes Johansson johjo76,gmail.com <owner= -chemistry^ccl.net> wrote:

From:= Johannes Johansson johjo76,gmail.com <owner-chemistry^ccl.net>
Su= bject: CCL:G: Is the ferromagentic state =3D the triplet state?
To: "Mes= a, Sayed " <elsayed.elmes^yahoo.com>
Date: Friday, Decembe= r 3, 2010, 2:03 AM

Dear Sayed,

I give my answers below.

Sincerely / Johannes
2010/12/2 elsayed elmeselhy elsay= ed.elmes]-[= yahoo.com <owner-chemistry[-]ccl.net>
=0A
Dear Dr. Adam,

=0AThanks for your response.= I would be appreciated if you clarified the following points:
1- "A closed-shell singlet state of this= system requires disproportionation to a Cu(I)-Cu(III) oxidation state."
=0A
My system is [Cu2L]4+ where L is macrocyclic ligand. Both co= pper cations have oxidation state =3D +2. Could you explain me how and why = the calculation of a closed-shell singlet state of my system  leads to disproportionation to a= Cu(I)-Cu(III) oxidation state. If there is a publication(s) refer to that = please, let me know.
=0A
= I was a bit too fast here. Does your system have a direct Cu-Cu bond? If so= , then I guess a closed-shell singlet state is possible even if both ions a= re in oxidation states with odd number of electrons. (I was thinking about = systems in which there is no direct bond between the copper ions, e.g. Cu-O= -O-Cu, which can not have a closed-shell singlet state with zero spin on bo= th Cu-atoms if these are Cu(II) since it is an odd number ion (d9). In such= systems, the only possibility to get a closed-shell singlet state is if th= e Cu(II)/Cu(II) oxidation state disproportionates to Cu(I)/Cu(III), most li= kely a high energy state.)
=0A

Is there any experim= ental data available for your system? Maybe for a similar system? Here is a= n exp ref for a bio-mimetic Cu(II)-O-O-Cu(II) complex, which has an antifer= romagnetic ground state: Karlin et al, JACS, 1993, 115, 2677. K= arlin and co-workers have done a lot of exp work on Cu-dimers so there migh= t be more interesting papers for you in his work.
=0A

 
<= tr>
=0A2- is the spin population ~1alfa on both Cu atoms in the= triplet state and =0A~1alfa and ~1beta on the Cu-atoms in the open-shell s= inglet state?
=0A
 
=
=0ADid you mean to s= ay open-shell triplet state  (~1alfa on both Cu atoms) and open-shell singlet state (~1alfa and ~1beta on the Cu-atoms= ), respectively?
=0A
Yes= (a triplet state is always open-shell).

=0A
In the first case, there are two alpha for Cu2+, then = it should be  open shell triplet state: In other word, in the input fi= le, we should fragment  the multiplicities of the molecule as the foll= owing:
=0A3 :the  multiplicity for whole complex (because the numbe= r of unpaired eletrons =3D 2)
2 : the multiplicity for the first Cu(2+) = (because the number of unpaired eletrons =3D1)
2 : the multiplicity for = the second Cu(2+) (because the number of unpaired eletrons =3D 1)
=0A1: = the multiplicity for ligand (because the number of unpaired eletrons =3D0)<= br>
Yes, but to get the trip= let state M=3D3 should be enough. To get the corresponding antiferromagneti= c coupling, these specifications might be necessary but then with M=3D1 for= the system as a whole. (I have not done this with Gaussian but is very eas= y with Jaguar or Turbomole.)
=0A

Good luck! / Johan= nes
 
=0A
Please let me = know your opinion=0A asap.

Regards,
Sayed

--- On Thu, 1= 2/2/10, Johannes Johansson johjo76..gmail.com <owner-chemistry-,-ccl.net> = wrote:
=0A

From: Johannes Johansson johjo76.= .gmail.com<= /a> <owner-chemistry-,-ccl.net>
=0ASubject: CCL: Is the ferromagentic state= =3D the triplet state?
To: "Mesa, Sayed " <elsayed.elmes-,-yahoo.com>Date: Thursday, December 2, 2010, 5:23 PM
=0A


Dear Sayed,

is the spin po= pulation ~1alfa on both Cu atoms in the triplet state and ~1alfa and ~1beta= on the Cu-atoms in the open-shell singlet state? If so, then these are the= ferro- and antiferromagnetically coupled states respectively. A closed-she= ll singlet state of this system requires disproportionation to a Cu(I)-Cu(I= II) oxidation state.
=0A=0A

Best regards / Johannes=  

--
Adam Johannes Johansson
Ph.D., M.= Sc.
Division of Physical Chemistry
KTH (Royal Institute of Technology= )
Teknikringen 36
=0ASE-100 44 Stockholm
Sweden
Office: 0879082= 17
=0ACell phone: 0708178487
E-mail:johjo76||gmai= l.com
Research web page:www.physto.se/~johjo
=0A
=0A=

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



--
Adam = Johannes Johansson
Ph.D., M.Sc.
Division of Physical Chemistry
KTH= (Royal Institute of Technology)
Teknikringen 36
SE-100 44 Stockholm<= br>Sweden
=0AOffice: 087908217
Cell phone: 0708178487
E-mail:johjo76[-]gmai= l.com
Research web page:www.physto.se/~johjo
=0A=0A=

=0A=0A --0-1243833806-1291345030=:7674-- From owner-chemistry@ccl.net Fri Dec 3 04:41:00 2010 From: "turker akcay turkerakcay[A]hotmail.com" To: CCL Subject: CCL:G: semiemprical calc. Message-Id: <-43267-101203043925-21269-XF4pxY5lL6qDWJ/X00zYDw a server.ccl.net> X-Original-From: "turker akcay" Date: Fri, 3 Dec 2010 04:39:23 -0500 Sent to CCL by: "turker akcay" [turkerakcay],[hotmail.com] Hi everybody I am trying to optimization on metal complexes. For Cu complex, I tried ONIOM methods (B3LYP/631G:PM3) and met an error message, so I used only PM3 method but met same error again. I could optimize Zn complex both ONIOM and PM3. I don't know what can I do. Could you help me. Best wishes... Error message Warning! Cu atom 209 has 11 valence electrons but only 4 basis functions. This is less than a minimal basis set! IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 209 NActive= 209 NUniq= 209 SFac= 1.00D+00 NAtFMM= 60 Big=T Leave Link 301 at Thu Nov 25 11:42:58 2010, MaxMem= 104857600 cpu: 0.0 (Enter C:\G03W\l401.exe) Simple Huckel Guess. NBasis= 620 NMin= 625 so simple Huckel guess is impossible. Error termination via Lnk1e in C:\G03W\l401.exe at Thu Nov 25 11:43:02 2010. Job cpu time: 0 days 0 hours 0 minutes 12.0 seconds. File lengths (MBytes): RWF= 52 Int= 0 D2E= 0 Chk= 1 Scr= 1 From owner-chemistry@ccl.net Fri Dec 3 05:15:00 2010 From: "Anup Thomas anupiict .. gmail.com" To: CCL Subject: CCL: regarding TDDFt Optimization in gaussian Message-Id: <-43268-101203045703-25854-oL06UMTwNkbLmtknmmkdIA=server.ccl.net> X-Original-From: "Anup Thomas" Date: Fri, 3 Dec 2010 04:57:00 -0500 Sent to CCL by: "Anup Thomas" [anupiict-,-gmail.com] I, Anup Thomas, a newbie in computational chemistry. Please answer me ? i would like to optimize the second Triplet state T2 using TDDFT but i am confused of keywords (my Seniors and i differ in some arguement) which one of the following is correct (Is there any differnce for these two approaches) #p b3lyp/6-31G* Td(triplets,root=2) opt title 0 1 geometry or #p b3lyp/6-31G* Td(triplets,root=1) opt title 0 3 geometry Look forward to hear from you all Thank you Anup Thomas From owner-chemistry@ccl.net Fri Dec 3 06:58:01 2010 From: "Thomas Gkourmpis thomas.gkourmpis-.-borealisgroup.com" To: CCL Subject: CCL:G: Problem with Transition State finder (QST3) in G09 Message-Id: <-43269-101203065652-16246-okD5Yr3S8UJDuB29pcPWNQ : server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Fri, 3 Dec 2010 06:56:50 -0500 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis-,-borealisgroup.com] Hello I am having a problem when I am trying to obtain a transition state using QST3 in Gaussian 09 in the presence of solvent (heptane and benzene), and any suggestion will be more than welcome. I am having a 2-(tert-butylperoxy)butoxy radical [(CH3)3-C-O-O-(CH3)(C2H5)C-O*] and I want to obtain the transition state in the cases where the CH3 and the C2H5 groups (attached to C-O*) are rearranging. When I do the calculation in the gas phase I get proper transition structures (one negative frequency) and the C-CH3 and C-C2H5 bonds are of the order of 1.9-2 (reasonable values). When I do the calculation in a solvent (heptane or benzene) I get transition structures (one negative frequency) but the equivalent bond lengths are of the order of 1.54 almost identical to the standard C-C bond length, something that cannot be correct. The input parameters I used for my model are %chk=chkpnt.chk #p opt=qst3 freq=noraman ub3lyp/6-311g(d,p) scrf=(solvent=benzene,read) with solvent parameters nosymcav OFac=0.8 RMin=0.5 In both cases the input for the calculation is the same except for the inclusion of the model, but the results are miles (or angstrom) appart. Any idea what I might be doing wrong? Thanks a lot in advance Thomas From owner-chemistry@ccl.net Fri Dec 3 07:40:00 2010 From: "Olli Lehtonen olehtone**chem.helsinki.fi" To: CCL Subject: CCL:G: ODP: CCL:G: ODP: CCL:G: Gaussian output problem Message-Id: <-43270-101203073748-29628-fbiJ8S24KCoLl+21ZxNysg*server.ccl.net> X-Original-From: Olli Lehtonen Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 3 Dec 2010 14:37:39 +0200 MIME-Version: 1.0 Sent to CCL by: Olli Lehtonen [olehtone[*]chem.helsinki.fi] Hi, Perhaps you have figured it out already by yourself, but adding a condition that resets the counter everytime new section is encountered will do the trick. For example BEGIN {atom=10000} { if (/^\ \*\*\*\*/) { sub("^\\ \\*\\*\\*\\*",atom); atom++; } print $0; if (/^\ 9999/) { atom=10000; } } So whenever line beginning with space and four 9's is encounterd, counter is reset to 10000. Take a look at awk manual page (man awk), there's plenty of sample scripts and documentation available in the www too. For more technical awk related discussion comp.lang.awk newsgroup maybe a better option. regards, Olli On Fri, Nov 26, 2010 at 10:03:15AM +0100, MASLYK, MACIEJ MARCIN maciejmarcin.maslyk__ceu.es wrote: > > Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk]_[ceu.es] > Thanks Olli, > the script is working. The thing is that in my input I have 200 sections with coordinates and this script changes stars for appropriate numbers in section 1 but in the second it doesn't change again from 10000 but continues from section 1. And so on. Do you know how to modify this script? > Example: > > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491169 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > > ble ble ble > > > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > > ble cble ble > > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > **** 8 20001021 37.587292 -11.572024 28.812192 > **** 1 20001030 37.333847 -11.927328 27.960694 > **** 1 20001030 38.095189 -12.272395 29.221488 > > ....... more then 200 times > > > So in every section of the file I want to have numbers from 10000 to ...... > > thanks > > regards > > Maciek > > > > Dr. Maciej Maslyk > Universidad San Pablo CEU > Urb. Montepríncipe, Ctra. Boadilla del Monte, > Km. 5.300, 28668 Madrid, España > Tel.- 91.372.64.31 - FAX.- 91.351.04.75 > ________________________________________ > Od: owner-chemistry+maciejmarcin.maslyk==ceu.es**ccl.net [owner-chemistry+maciejmarcin.maslyk==ceu.es**ccl.net] w imieniu Olli Lehtonen olehtone]~[chem.helsinki.fi [owner-chemistry**ccl.net] > Wysłano: 24 listopada 2010 13:12 > Do: MASLYK, MACIEJ MARCIN > Temat: CCL:G: ODP: CCL:G: Gaussian output problem > > Sent to CCL by: Olli Lehtonen [olehtone . chem.helsinki.fi] > Hi, > > Apparently you are using linux so with scripting language awk you can write > > BEGIN {atom=10000} > > { if (/^\ \*\*\*\*/) { > sub("^\\ \\*\\*\\*\\*",atom); > atom++; > } > print $0; > } > > Assuming that script is contained in file called stars.awk you then give a > command (output follows) > > awk -f stars.awk test.out > 9995 1 20001030 -12.655571 46.600810 32.540627 > 9996 1 20001030 -12.533484 47.134581 33.952118 > 9997 8 20001021 2.441067 -19.529269 31.331119 > 9998 1 20001030 2.813824 -19.307495 32.184450 > 9999 1 20001030 1.933916 -20.325103 31.491166 > 10000 8 20001021 37.587292 -11.572024 28.812192 > 10001 1 20001030 37.333847 -11.927328 27.960694 > 10002 1 20001030 38.095189 -12.272395 29.221488 > 10003 8 20001021 23.735956 -43.072924 13.135294 > 10004 1 20001030 23.388276 -42.182008 13.115359 > 10005 1 20001030 22.974070 -43.624340 13.312930 > > where test.out contains your sample output. > > Just be aware that the script changes all **** (in the beginning of line > with one extra space) with the running number so if you have the same > problem someplace else in the output file it will change it there too. > > Hope it helps, > > Olli > > > Oe Wed, Nov 24, 2010 at 10:20:47AM +0100, MASLYK, MACIEJ MARCIN maciejmarcin.maslyk^-^ceu.es wrote: > > > > Sent to CCL by: "MASLYK, MACIEJ MARCIN" [maciejmarcin.maslyk!A!ceu.es] > > Thanks for help but I'm completely begginer in gaussian and also in linux so can you guys explain this thing with source code more precisely, please? > > > > Sam, I got 15 k atoms and 250 steps so it will kill me if I start changing stars to numbers manually :) > > > > regards > > > > Maciek > > > > -----Original Message----- > > > From: owner-chemistry+closed==etsu.edu__ccl.net [mailto:owner-chemistry+closed==etsu.edu__ccl.net] On Behalf Of Maciej Maslyk maciejmarcin.maslyk .. ceu.es > > Sent: Tuesday, November 23, 2010 8:45 AM > > To: Close, David M. > > Subject: CCL:G: Gaussian output problem > > > > > > Sent to CCL by: "Maciej Maslyk" [maciejmarcin.maslyk-,-ceu.es] > > Hi everyone, > > could you help me with one problem, please? Every time I'm running G03 job I got problem with outputs. The problem is that I cannot extract structures because there are stars **** instead of atom numbers higher than 9999. Have you ever had this problem in your calculation if you had more than 9999 atoms in the system? > > > > It looks like this in output: > > 9995 1 20001030 -12.655571 46.600810 32.540627 > > 9996 1 20001030 -12.533484 47.134581 33.952118 > > 9997 8 20001021 2.441067 -19.529269 31.331119 > > 9998 1 20001030 2.813824 -19.307495 32.184450 > > 9999 1 20001030 1.933916 -20.325103 31.491166 > > **** 8 20001021 37.587292 -11.572024 28.812192 > > **** 1 20001030 37.333847 -11.927328 27.960694 > > **** 1 20001030 38.095189 -12.272395 29.221488 > > **** 8 20001021 23.735956 -43.072924 13.135294 > > **** 1 20001030 23.388276 -42.182008 13.115359 > > **** 1 20001030 22.974070 -43.624340 13.312930 > > > > Do you have any suggestions? > > > > Thanks in advancehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Fri Dec 3 08:15:00 2010 From: "Ivo Jacobs jacobs.ivo!A!gmail.com" To: CCL Subject: CCL:G: a question regarding TS finding in g03 Message-Id: <-43271-101203034843-4991-763Fwc+5a3NIk5Ahf+FWzQ:_:server.ccl.net> X-Original-From: Ivo Jacobs Content-Type: multipart/alternative; boundary="------------050107060800010300030500" Date: Fri, 03 Dec 2010 09:48:34 +0100 MIME-Version: 1.0 Sent to CCL by: Ivo Jacobs [jacobs.ivo_-_gmail.com] This is a multi-part message in MIME format. --------------050107060800010300030500 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hello, I would say that you have definately found a transition state, but you should make sure that it is indeed the transition state that you are interested in. First of all you can visualise the negative vibration with gausview to make sure that it corresponds to the right reaction coordinate. Then to be absolutely sure you should do a IRC calculation to find the two minima that are connected to this transition state. Good luck, Ivo Jacobs On 3-12-10 4:49 AM, Li qiang cougarhead_2003||yahoo.com wrote: > Hi CCL'ers: > > I have a somewhat strange TS locating problem wtih g03. My first run > of locating the TS was completed fine, with the output of the > optimized TS coordinates: > > Input orientation: > --------------------------------------------------------------------- > Center Atomic Atomic Coordinates (Angstroms) > Number Number Type X Y Z > --------------------------------------------------------------------- > 1 9 0 -3.386882 1.262162 -0.189094 > 2 1 0 -4.252089 0.740968 0.231843 > 3 17 0 -5.482326 -0.002357 0.832002 > --------------------------------------------------------------------- > > because I saw the convergence in the optimization is: > Item Value Threshold Converged? > Maximum Force 0.000032 0.000450 YES > RMS Force 0.000022 0.000300 YES > Maximum Displacement 0.000697 0.001800 YES > RMS Displacement 0.000666 0.001200 YES > Predicted change in Energy=-1.988338D-08 > Optimization completed. > -- Stationary point found. > > And the link1 freq calculation shows: > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering > activities (A**4/AMU), depolarization ratios for plane and unpolarized > incident light, reduced masses (AMU), force constants (mDyne/A), > and normal coordinates: > 1 2 3 > A A A > Frequencies -- -2672.6281 525.4568 578.5686 > Red. masses -- 1.0263 22.2631 1.0304 > Frc consts -- 4.3194 3.6217 0.2032 > IR Inten -- 7645.8759 16.4800 57.7877 > Atom AN X Y Z X Y Z X Y > Z > 1 9 -0.02 -0.01 0.01 0.68 0.42 -0.34 -0.02 0.02 > -0.01 > 2 1 0.79 0.48 -0.38 0.14 -0.01 0.00 0.61 -0.65 > 0.45 > 3 17 -0.01 -0.01 0.01 -0.38 -0.23 0.18 -0.01 0.01 > -0.01 > > However, if I tried to start over to do a TS locating calculation > using the same theory/basis-level uhf/sto-3g > opt(TS,calcall,noeigentest) nosymm as I used in obtaining the > stationary point and the freq calculation as above, the job continued > to run, seemingly to confirm the TS point found previously was not the > correct one. Could anyone please suggest what might go wrong here? It > is a very short run of g03; hope you can pleasea let me know what you > may get. > > Thanks a lot! > > --------------050107060800010300030500 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hello,

I would say that you have definately found a transition state, but you should make sure that it is indeed the transition state that you are interested in. First of all you can visualise the negative vibration with gausview to make sure that it corresponds to the right reaction coordinate. Then to be absolutely sure you should do a IRC calculation to find the two minima that are connected to this transition state.

Good luck,
Ivo Jacobs


On 3-12-10 4:49 AM, Li qiang cougarhead_2003||yahoo.com wrote:
Hi CCL'ers:

I have a somewhat strange TS locating problem wtih g03. My first run of locating the TS was completed fine, with the output of the optimized TS coordinates:

                          Input orientation:                          
 ---------------------------------------------------------------------
 Center     Atomic     Atomic              Coordinates (Angstroms)
 Number     Number      Type              X           Y           Z
 ---------------------------------------------------------------------
    1          9             0       -3.386882    1.262162   -0.189094
    2          1             0       -4.252089    0.740968    0.231843
    3         17             0       -5.482326   -0.002357    0.832002
 ---------------------------------------------------------------------

because I saw the convergence in the optimization is:
         Item               Value     Threshold  Converged?
 Maximum Force            0.000032     0.000450     YES
 RMS     Force            0.000022     0.000300     YES
 Maximum Displacement     0.000697     0.001800     YES
 RMS     Displacement     0.000666     0.001200     YES
 Predicted change in Energy=-1.988338D-08
 Optimization completed.
    -- Stationary point found.

And the link1 freq calculation shows:
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
 activities (A**4/AMU), depolarization ratios for plane and unpolarized
 incident light, reduced masses (AMU), force constants (mDyne/A),
 and normal coordinates:
                     1                      2                      3
                     A                      A                      A
 Frequencies -- -2672.6281               525.4568               578.5686
 Red. masses --     1.0263                22.2631                 1.0304
 Frc consts  --     4.3194                 3.6217                 0.2032
 IR Inten    --  7645.8759                16.4800                57.7877
 Atom AN      X      Y      Z        X      Y      Z        X      Y      Z
   1   9    -0.02  -0.01   0.01     0.68   0.42  -0.34    -0.02   0.02  -0.01
   2   1     0.79   0.48  -0.38     0.14  -0.01   0.00     0.61  -0.65   0.45
   3  17    -0.01  -0.01   0.01    -0.38  -0.23   0.18    -0.01   0.01  -0.01

However, if I tried to start over to do a TS locating calculation using the same theory/basis-level uhf/sto-3g opt(TS,calcall,noeigentest) nosymm as I used in obtaining the stationary point and the freq calculation as above, the job continued to run, seemingly to confirm the TS point found previously was not the correct one. Could anyone please suggest what might go wrong here? It is a very short run of g03; hope you can pleasea let me know what you may get.

Thanks a lot!


--------------050107060800010300030500-- From owner-chemistry@ccl.net Fri Dec 3 08:50:00 2010 From: "WATOC watoc2011~!~uam.es" To: CCL Subject: CCL: WATOC 2011 - Important News Message-Id: <-43272-101203033552-5281-quXDoKIT0lD9i1OBw+XIBg---server.ccl.net> X-Original-From: "WATOC " Date: Fri, 3 Dec 2010 03:35:48 -0500 Sent to CCL by: "WATOC " [watoc2011(~)uam.es] *With apologies for any possible cross-posting* Dear Colleagues, we are pleased to announce that the Registration for WATOC-2011 as well as abstracts submission will be opened next December 13th. The deadline for early registration is April, 1st, 2011, and for abstracts submission March, 1st, 2011 We invite you to visit our website: www.watoc2011.com and see the list of Invited speakers who have already accepted to participate. ACCOMMODATION Specially for Ph.D. students (although they are available for all participants), we are offering very cheap and convenient accommodation in University Residences: 407 single rooms and 13 double rooms, all of them with the bathroom inside the room. The Burgo das Nacions Residence (290 single room) (http://www.usc.es/es/servizos/sur/residencias/burgo/index.html) is just in front of the Auditorio de Galicia, and 7 minutes walking distance from the Faculty of Medicine. The Rodriguez Cadarso Residence (42 single rooms and 5 double rooms) (http://www.usc.es/es/servizos/sur/residencias/cadarso/index.html) has been recently rebuilt and is 15 minutes walking distance from the Faculty of Medicine and 22 minutes from the Auditorio de Galicia. San Agustn Residence (75 single rooms and 8 double rooms) is in the old town, 7 minutes walking distance from the Faculty of Medicine. We also offer a good variety of Hotels, most of them at walking distance of the Faculty of Medicine or of the Auditorio de Galicia (in particular Hotel San Francisco, Hospedera San Martn Pinario and NH Obradoiro Hotel). See the complete list and their locations at the WATOC-2011 website. LUNCHES We are offering also 400 lunches/day in Hospedera San Martin Pinario (http://www.sanmartinpinario.eu/), a brand-new hotel just across the street of the Faculty of Medicine and in front of the Cathedral. This Hotel is installed in the second largest Monastery (XVI Century) of Spain (after El Escorial near Madrid). The dining room is the refectory of the old Monastery, thereby offering a magnificent environment and very good food at a reasonable price. This offering is made on a first-come-first-served base. Therefore if you are interested please book this service as soon as possible. SOCIAL EVENTS The Banquet will take place at Pazo de San Lorenzo an amazingly beautiful Galician Palace from the XIII-XVII Centuries (http://www.pazodesanlorenzo.com/) An excursion will be organized to visit the wonderful Galicias coast (Ras Baixas), including a boat trip along one of the most beautiful Ras (Ra de Arousa). Mussels and white wine will be served on the boat. The excursion is included in the Registration Fee. Tickets will be available for accompanying persons. A concert, whose details will be announced in due time, will be also offered to all participants and accompanying persons free of charge. ABSTRACT SUBMISSION The deadline for the submission of abstracts is March, 1st, 2011. The submission procedure is fully explained in the website. SATELLITE MEETINGS Three satellite meetings will be organized, one before and two after WATOC: Theoretical modeling of materials. A workshop aimed at sharing expertise and strategies in handling inorganic, organic and biomaterials. Barcelona July 13-15th 2011, Aula Magna Enric Casassas, Facultat de Qumica, Universitat de Barcelona Scientific Committee: Francesc Illas (IQTCUB); Juan J. Novoa (IQTCUB); Mariona Sodupe (Universitat Autonoma de Barcelona); Javier Fernandez Sanz (Universidad de Sevilla) Excited states and non-adiabatic processes in complex systems. Theoretical approaches Girona (Spain) 25 - 27 july 2011 Scientific Committee: Llus Blancafort (University of Girona); Mar Reguero (University of Tarragona); Carles Curutchet (University of Girona) Strongly correlated systems, cooperativity, and valence-bond theory A Corua (Spain) 23-25 July 2011 Chairman: Josep M. Oliva More information about these satellites in our webpage: www.watoc2011.com Manuel Yanez and Otilia Mo Departamento de Qumica, C-IX Univerisdad Autnoma de Madrid Cantoblanco, 28049-Madrid. Spain Phone: +34-497-4953 Fax: +34-497-5238 Emails: manuel.yanez*o*uam.es; otilia.mo*o*uam.es From owner-chemistry@ccl.net Fri Dec 3 09:25:00 2010 From: "Mike Devereux mike.devereux_+_parisdescartes.fr" To: CCL Subject: CCL:G: TD-DFT Issue Message-Id: <-43273-101203064107-3848-UD4WOf3lUC3XjU5Y/GXvvA-*-server.ccl.net> X-Original-From: "Mike Devereux" Date: Fri, 3 Dec 2010 06:41:04 -0500 Sent to CCL by: "Mike Devereux" [mike.devereux..parisdescartes.fr] Dear all, I find myself working with an experimental group, and using TD-DFT for the first time to simulate UV-VIS absorption spectra. In writing up the results we obtained to submit to an inroganic chemistry journal and I need to explain concisely what the CI coefficients listed by Gaussian09 mean, and why we have the same orbitals involved in two transitions at separate energies: Excited State 5: Singlet-A 2.7803 eV 445.93 nm f=0.2938 =0.000 167 ->171 0.48665 168 ->170 0.47616 169 ->172 -0.17314 Excited State 11: Singlet-A 3.0206 eV 410.47 nm f=0.1839 =0.000 167 ->171 0.11921 168 ->170 0.12063 169 ->172 0.68196 My understanding is that the CI coefficients listed show those orbitals from the ground state wave function that mix (interact) most strongly with those in the corresponding excited state wave function in the presence of the oscillating external field of the stated frequency. Firstly, is this interpretation accurate, and secondly does anyone know of a good citation I could add here? Many thanks in advance for any advice! Regards, Mike Devereux From owner-chemistry@ccl.net Fri Dec 3 11:29:00 2010 From: "Li qiang cougarhead_2003#yahoo.com" To: CCL Subject: CCL:G: a question regarding TS finding in g03 Message-Id: <-43274-101203112543-30936-yw8hR3V2ZxXarDhwHrdAMw#server.ccl.net> X-Original-From: Li qiang Content-Type: multipart/alternative; boundary="0-1444482399-1291393522=:32026" Date: Fri, 3 Dec 2010 08:25:22 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Li qiang [cougarhead_2003-.-yahoo.com] --0-1444482399-1291393522=:32026 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Ivo, Thank you for your reply. But you probably did not answer the part I feel p= uzzled.=20 I know how to identify whether the transition state optimization in g03 get= s the imaginary freq and how to visualize it etc. and how to confirm the wh= ether it is related to the intended reaction by doing an IRC calculation.= =20 However, my questions is: why the optimized transition state structure obta= ined by one successful g03 run could not be confirmed in the second g03 run= when the final optimized structure was given as the input? Thank you again and anyone who may post an answer. --- On Fri, 12/3/10, Ivo Jacobs jacobs.ivo!A!gmail.com wrote: > From: Ivo Jacobs jacobs.ivo!A!gmail.com Subject: CCL:G: a question regarding TS finding in g03 To: "Li, Qiang " Date: Friday, December 3, 2010, 3:48 AM =0A=0A =0A=0A =0A =0A Hello, =0A =20 =0A I would say that you have definately found a transition state, but= =0A you should make sure that it is indeed the transition state that you= =0A are interested in. First of all you can visualise the negative=0A = vibration with gausview to make sure that it corresponds to the=0A righ= t reaction coordinate. Then to be absolutely sure you should do=0A a IRC= calculation to find the two minima that are connected to this=0A transi= tion state. =0A =20 =0A Good luck, =0A Ivo Jacobs =0A =20 =0A =20 =0A On 3-12-10 4:49 AM, Li qiang cougarhead_2003||yahoo.com wrote:=0A = =0A =0A =0A =0A Hi CCL'ers: =0A =20 =0A I have a somewhat strange TS locating problem wtih g03. My= =0A first run of locating the TS was completed fine, with the= =0A output of the optimized TS coordinates: =0A =20 =0A =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Input = orientation: =A0 =A0 =A0 =A0 =A0 =A0 =A0=0A =A0 =A0 =A0 =A0 = =A0 =A0=20 =0A =A0-------------------------------------------------------= --------------=0A =20 =0A =A0Center =A0 =A0 Atomic =A0 =A0 Atomic =A0 =A0 =A0 =A0 = =A0 =A0 =A0Coordinates=0A (Angstroms)=20 =0A =A0Number =A0 =A0 Number =A0 =A0 =A0Type =A0 =A0 =A0 =A0 = =A0 =A0 =A0X =A0 =A0 =A0 =A0 =A0 Y =A0=0A =A0 =A0 =A0 =A0 Z=20 =0A =A0-------------------------------------------------------= --------------=0A =20 =0A =A0 =A0 1 =A0 =A0 =A0 =A0 =A09 =A0 =A0 =A0 =A0 =A0 =A0 0 = =A0 =A0 =A0 -3.386882 =A0 =A01.262162=0A =A0 -0.189094=20 =0A =A0 =A0 2 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 0 = =A0 =A0 =A0 -4.252089 =A0 =A00.740968=0A =A0 =A00.231843=20 =0A =A0 =A0 3 =A0 =A0 =A0 =A0 17 =A0 =A0 =A0 =A0 =A0 =A0 0 =A0= =A0 =A0 -5.482326 =A0 -0.002357=0A =A0 =A00.832002=20 =0A =A0-------------------------------------------------------= --------------=0A =20 =0A =20 =0A because I saw the convergence in the optimization is: =0A =A0 =A0 =A0 =A0=A0 Item =A0 =A0 =A0 =A0 =A0 =A0 =A0 Value = =A0 =A0 Threshold=0A =A0Converged?=20 =0A =A0Maximum Force =A0 =A0 =A0 =A0 =A0 =A00.000032 =A0 =A0 0= .000450 =A0 =A0 YES=20 =0A =A0RMS =A0 =A0 Force =A0 =A0 =A0 =A0 =A0 =A00.000022 =A0 = =A0 0.000300 =A0 =A0 YES=20 =0A =A0Maximum Displacement =A0 =A0 0.000697 =A0 =A0 0.001800 = =A0 =A0 YES=20 =0A =A0RMS =A0 =A0 Displacement =A0 =A0 0.000666 =A0 =A0 0.001= 200 =A0 =A0 YES=20 =0A =A0Predicted change in Energy=3D-1.988338D-08=20 =0A =A0Optimization completed.=20 =0A =A0 =A0 -- Stationary point found.=20 =0A =20 =0A And the link1 freq calculation shows: =0A Harmonic frequencies (cm**-1), IR intensities (KM/Mole),= =0A Raman scattering=20 =0A =A0activities (A**4/AMU), depolarization ratios for plane= =0A and unpolarized=20 =0A =A0incident light, reduced masses (AMU), force constants= =0A (mDyne/A),=20 =0A =A0and normal coordinates:=20 =0A =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0=0A = =A0 =A0 =A0 =A0 =A03=20 =0A =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0A =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0A =A0 =A0 =A0 =A0 =A0 =A0=0A = =A0 =A0 =A0 =A0 =A0A=20 =0A =A0Frequencies -- -2672.6281 =A0 =A0 =A0 =A0 =A0 =A0 =A0 5= 25.4568 =A0 =A0 =A0 =A0=0A =A0 =A0 =A0 578.5686=20 =0A =A0Red. masses -- =A0 =A0 1.0263 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A022.2631 =A0 =A0 =A0 =A0=0A =A0 =A0 =A0 =A0 1.0304=20 =0A =A0Frc consts =A0-- =A0 =A0 4.3194 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 3.6217 =A0 =A0 =A0 =A0=0A =A0 =A0 =A0 =A0 0.2032=20 =0A =A0IR Inten =A0 =A0-- =A07645.8759 =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A016.4800 =A0 =A0 =A0 =A0=0A =A0 =A0 =A0 =A057.7877=20 =0A =A0Atom AN =A0 =A0 =A0X =A0 =A0 =A0Y =A0 =A0 =A0Z =A0 =A0 = =A0 =A0X =A0 =A0 =A0Y =A0 =A0 =A0Z =A0 =A0 =A0=0A =A0X =A0 =A0= =A0Y =A0 =A0 =A0Z=20 =0A =A0 =A01 =A0 9 =A0 =A0-0.02 =A0-0.01 =A0 0.01 =A0 =A0 0.68= =A0 0.42 =A0-0.34 =A0=0A =A0-0.02 =A0 0.02 =A0-0.01=20 =0A =A0 =A02 =A0 1 =A0 =A0 0.79 =A0 0.48 =A0-0.38 =A0 =A0 0.14= =A0-0.01 =A0 0.00 =A0 =A0=0A 0.61 =A0-0.65 =A0 0.45=20 =0A =A0 =A03 =A017 =A0 =A0-0.01 =A0-0.01 =A0 0.01 =A0 =A0-0.38= =A0-0.23 =A0 0.18 =A0=0A =A0-0.01 =A0 0.01 =A0-0.01=20 =0A =20 =0A However, if I tried to start over to do a TS locating=0A = calculation using the same theory/basis-level uhf/sto-3g=0A = opt(TS,calcall,noeigentest) nosymm as I used in obtaining=0A = the stationary point and the freq calculation as above,=0A = the job continued to run, seemingly to confirm the TS=0A = point found previously was not the correct one. Could=0A anyo= ne please suggest what might go wrong here? It is a=0A very sh= ort run of g03; hope you can pleasea let me know=0A what you m= ay get. =0A =20 =0A Thanks a lot! =0A =20 =0A =0A =0A =0A =0A =20 =0A =0A =20 =0A =0A=0A=0A=0A --0-1444482399-1291393522=:32026 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Ivo,

Thank you for your reply. But = you probably did not answer the part I feel puzzled.

I know how to = identify whether the transition state optimization in g03 gets the imaginar= y freq and how to visualize it etc. and how to confirm the whether it is re= lated to the intended reaction by doing an IRC calculation.

However= , my questions is: why the optimized transition state structure obtained by= one successful g03 run could not be confirmed in the second g03 run when t= he final optimized structure was given as the input?

Thank you again= and anyone who may post an answer.


--- On Fri, 12/3/10, Ivo = Jacobs jacobs.ivo!A!gmail.com <owner-chemistry- -ccl.net> wr= ote:

From: Ivo Jacobs jacobs.ivo!A!gmail.co= m <owner-chemistry- -ccl.net>
Subject: CCL:G: a question regarding TS= finding in g03
To: "Li, Qiang " <cougarhead_2003- -yahoo.com&g= t;
Date: Friday, December 3, 2010, 3:48 AM

=0A=0A =0A=0A =0A =0A Hello,
=0A
=0A = I would say that you have definately found a transition state, but=0A = you should make sure that it is indeed the transition state that you=0A = are interested in. First of all you can visualise the negative=0A vibrat= ion with gausview to make sure that it corresponds to the=0A right react= ion coordinate. Then to be absolutely sure you should do=0A a IRC calcul= ation to find the two minima that are connected to this=0A transition st= ate.
=0A
=0A Good luck,
=0A Ivo Jacobs
=0A
=0A=
=0A On 3-12-10 4:49 AM, Li qiang cougarhead_2003||yahoo.com wrot= e:=0A
=0A =0A =0A =0A = =0A = =0A =0A
Hi CCL'ers:
=0A =
=0A I have a somewhat strange TS locating problem wtih g0= 3. My=0A first run of locating the TS was completed fine, with= the=0A output of the optimized TS coordinates:
=0A =
=0A              =             Input orientation:    =          =0A       &n= bsp;    
=0A  -----------------------------= ----------------------------------------=0A
=0A =  Center     Atomic     Atomic     &nb= sp;        Coordinates=0A (Angstroms)
= =0A  Number     Number      Type=              X       &nb= sp;   Y  =0A         Z
=0A =  ---------------------------------------------------------= ------------=0A
=0A     1   &n= bsp;      9             0 &nbs= p;     -3.386882    1.262162=0A   -0.= 189094
=0A     2         &nb= sp;1             0       -4.25= 2089    0.740968=0A    0.231843
=0A =     3         17     &nb= sp;       0       -5.482326   -0.002357= =0A    0.832002
=0A  ---------= ------------------------------------------------------------=0A =
=0A
=0A because I saw the convergence i= n the optimization is:
=0A         = ; Item               Value    = Threshold=0A  Converged?
=0A  Maxi= mum Force            0.000032     0= .000450     YES
=0A  RMS     Forc= e            0.000022     0.000300 =     YES
=0A  Maximum Displacement   &n= bsp; 0.000697     0.001800     YES
=0A =  RMS     Displacement     0.000666     = 0.001200     YES
=0A  Predicted change in E= nergy=3D-1.988338D-08
=0A  Optimization completed. =0A     -- Stationary point found.
=0A =
=0A And the link1 freq calculation shows:
=0A = Harmonic frequencies (cm**-1), IR intensities (KM/Mole),=0A = Raman scattering
=0A  activities (A**4/AMU), = depolarization ratios for plane=0A and unpolarized
=0A =  incident light, reduced masses (AMU), force constants=0A = (mDyne/A),
=0A  and normal coordinates: =0A                 =      1               &nbs= p;      2            =0A =          3
=0A   &nb= sp;                  A   =                    A &nbs= p;          =0A       =    A
=0A  Frequencies -- -2672.6281   =             525.4568       &nb= sp;=0A       578.5686
=0A &nbs= p;Red. masses --     1.0263           &n= bsp;    22.2631        =0A  = ;       1.0304
=0A  Frc consts  -= -     4.3194               &nb= sp; 3.6217        =0A      =   0.2032
=0A  IR Inten    --  76= 45.8759                16.4800 &nbs= p;      =0A        57.7877 =
=0A  Atom AN      X     &nbs= p;Y      Z        X      = Y      Z      =0A  X  =    Y      Z
=0A    1 &= nbsp; 9    -0.02  -0.01   0.01     0.68  = ; 0.42  -0.34  =0A  -0.02   0.02  -0.= 01
=0A    2   1     0.79   0= .48  -0.38     0.14  -0.01   0.00    =0A= 0.61  -0.65   0.45
=0A   &nbs= p;3  17    -0.01  -0.01   0.01    -0.38 =  -0.23   0.18  =0A  -0.01   0.01 &nbs= p;-0.01
=0A
=0A However, if I tried to st= art over to do a TS locating=0A calculation using the same the= ory/basis-level uhf/sto-3g=0A opt(TS,calcall,noeigentest) nosy= mm as I used in obtaining=0A the stationary point and the freq= calculation as above,=0A the job continued to run, seemingly = to confirm the TS=0A point found previously was not the correc= t one. Could=0A anyone please suggest what might go wrong here= ? It is a=0A very short run of g03; hope you can pleasea let m= e know=0A what you may get.
=0A
=0A = Thanks a lot!
=0A
=0A
=0A
=0A =0A
=0A =0A

=0A=0A=0A=0A= =0A=0A=0A=0A --0-1444482399-1291393522=:32026-- From owner-chemistry@ccl.net Fri Dec 3 12:51:01 2010 From: "Jens Spanget-Larsen spanget\a/ruc.dk" To: CCL Subject: CCL:G: TD-DFT Issue Message-Id: <-43275-101203124824-22264-vPl+R4nzmpiZZ97CD6T/2A*o*server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Type: multipart/alternative; boundary="------------020601050809050406040504" Date: Fri, 03 Dec 2010 18:48:09 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget:_:ruc.dk] This is a multi-part message in MIME format. --------------020601050809050406040504 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Mike Devereux! The listing i --> j indicates the excited electronic configuration that is derived by promotion of an electron from the i'th MO to the j'th MO, where the i'th MO is one of the occupied, and the j-th MO one of the unoccupied (Kohn-Sham) orbitals in the electronic ground state. In the configuration interaction (CI) model of the excited electronic states, these configurations are allowed to interact, thereby yielding a description of the excited states in terms of linear combinations of electronic configurations. The listed CI coefficents indicate the contributions from the various configurations to the excited state in question. In ~general, the percentage contribution is obtained by the expression 100*2*C*C, where C is the printed coefficient. An example > from your mail: In the case of excited state no. 5, the coefficient of the configuration listed as 169-->172 is -0.17314, amounting to a contribution of 6%. For excited state no. 11, the corresponding coefficient is 0.68196, indicating a contribution of 93%. Yours, Jens >--< PS. Several reviews on the calculation of excited electronic states and electronic transitions have been published, for example by S. Grimme, in: K.B. Lipkowitz, R. Larter, T.R. Cundari (Eds.), Reviews in Computational Chemistry, vol. 20, Wiley-VCH, Weinheim, 2008, pp. 153-217. ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget#ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ On 12/3/2010 12:41, Mike Devereux mike.devereux_+_parisdescartes.fr wrote: > Sent to CCL by: "Mike Devereux" [mike.devereux..parisdescartes.fr] > Dear all, > > I find myself working with an experimental group, and using TD-DFT for the first time to simulate UV-VIS absorption spectra. In writing up the results we obtained to submit to an inroganic chemistry journal and I need to explain concisely what the CI coefficients listed by Gaussian09 mean, and why we have the same orbitals involved in two transitions at separate energies: > > Excited State 5: Singlet-A 2.7803 eV 445.93 nm f=0.2938=0.000 > 167 ->171 0.48665 > 168 ->170 0.47616 > 169 ->172 -0.17314 > > Excited State 11: Singlet-A 3.0206 eV 410.47 nm f=0.1839=0.000 > 167 ->171 0.11921 > 168 ->170 0.12063 > 169 ->172 0.68196 > > My understanding is that the CI coefficients listed show those orbitals from the ground state wave function that mix (interact) most strongly with those in the corresponding excited state wave function in the presence of the oscillating external field of the stated frequency. Firstly, is this interpretation accurate, and secondly does anyone know of a good citation I could add here? > > Many thanks in advance for any advice! > > Regards, > Mike Devereux> > --------------020601050809050406040504 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit 
Dear Mike Devereux!
The listing i --> j indicates the excited electronic configuration that is derived by promotion of an electron from the i'th MO to the j'th MO, where the i'th MO is one of the occupied, and the j-th MO one of the unoccupied (Kohn-Sham) orbitals in the electronic ground state. In the configuration interaction (CI) model of the excited electronic states, these configurations are allowed to interact, thereby yielding a description of the excited states in terms of linear combinations of electronic configurations. The listed CI coefficents indicate the contributions from the various configurations to the excited state in question. In ~general, the percentage contribution is obtained by the expression 100*2*C*C, where C is the printed coefficient. An example from your mail: In the case of excited state no. 5, the coefficient of the configuration listed as 169-->172 is -0.17314, amounting to a contribution of 6%. For excited state no. 11, the corresponding coefficient is 0.68196, indicating a contribution of 93%.

Yours, Jens >--<

PS. Several reviews on the calculation of excited electronic states and electronic transitions have been published, for example by S. Grimme, in: K.B. Lipkowitz, R. Larter, T.R. Cundari (Eds.), Reviews in Computational Chemistry, vol. 20, Wiley-VCH, Weinheim, 2008, pp. 153-217. 
  ------------------------------------------------------
  JENS SPANGET-LARSEN         Office:      +45 4674 2710
  Dept. of Science (18.1)     Fax:         +45 4674 3011
  Roskilde University         Mobile:      +45 2320 6246
  P.O.Box 260                 E-Mail:     spanget#ruc.dk
  DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
  ------------------------------------------------------

On 12/3/2010 12:41, Mike Devereux mike.devereux_+_parisdescartes.fr wrote: 
Sent to CCL by: "Mike  Devereux" [mike.devereux..parisdescartes.fr]
Dear all,

I find myself working with an experimental group, and using TD-DFT for the first time to simulate UV-VIS absorption spectra. In writing up the results we obtained to submit to an inroganic chemistry journal and I need to explain concisely what the CI coefficients listed by Gaussian09 mean, and why we have the same orbitals involved in two transitions at separate energies:

 Excited State   5:      Singlet-A      2.7803 eV  445.93 nm  f=0.2938  <S**2>=0.000
     167 ->171         0.48665
     168 ->170         0.47616
     169 ->172        -0.17314

 Excited State  11:      Singlet-A      3.0206 eV  410.47 nm  f=0.1839  <S**2>=0.000
     167 ->171         0.11921
     168 ->170         0.12063
     169 ->172         0.68196

My understanding is that the CI coefficients listed show those orbitals from the ground state wave function that mix (interact) most strongly with those in the corresponding excited state wave function in the presence of the oscillating external field of the stated frequency. Firstly, is this interpretation accurate, and secondly does anyone know of a good citation I could add here?

Many thanks in advance for any advice!

Regards,
Mike DevereuxE-mail to subscribers: CHEMISTRY#ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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--------------020601050809050406040504-- From owner-chemistry@ccl.net Fri Dec 3 13:26:00 2010 From: "Mark Zottola mzottola:+:gmail.com" To: CCL Subject: CCL:G: a question regarding TS finding in g03 Message-Id: <-43276-101203131338-8507-x/DI9dy06er9F1Z7VOcGag . server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=00163692008ae136810496857e9a Date: Fri, 3 Dec 2010 13:13:30 -0500 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola%%gmail.com] --00163692008ae136810496857e9a Content-Type: text/plain; charset=ISO-8859-1 Li, Why did you use the noeigentest? If you do not allow the optimizer to check if it is going to a saddle point or to a minimum, then the optimization will proceed in some direction. You may have asked for a TS, but since the optimizer cannot determine where it is going, then you will probably end up some place other than where you wanted. SOmething else... did you check the convergence criteria after the frequency calculation? Sometimes an optimization says it has reached a stationary point, only to find out that the newly calculated Hessian says you are still an optimization step or two away. And this would explain why, in conjunction with the noeigentest, your optimization continues. Hope this helps... Mark I cannot totally say why you observe this, but On Thu, Dec 2, 2010 at 10:49 PM, Li qiang cougarhead_2003||yahoo.com < owner-chemistry__ccl.net> wrote: > Hi CCL'ers: > > I have a somewhat strange TS locating problem wtih g03. My first run of > locating the TS was completed fine, with the output of the optimized TS > coordinates: > > Input orientation: > --------------------------------------------------------------------- > Center Atomic Atomic Coordinates (Angstroms) > Number Number Type X Y Z > --------------------------------------------------------------------- > 1 9 0 -3.386882 1.262162 -0.189094 > 2 1 0 -4.252089 0.740968 0.231843 > 3 17 0 -5.482326 -0.002357 0.832002 > --------------------------------------------------------------------- > > because I saw the convergence in the optimization is: > Item Value Threshold Converged? > Maximum Force 0.000032 0.000450 YES > RMS Force 0.000022 0.000300 YES > Maximum Displacement 0.000697 0.001800 YES > RMS Displacement 0.000666 0.001200 YES > Predicted change in Energy=-1.988338D-08 > Optimization completed. > -- Stationary point found. > > And the link1 freq calculation shows: > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering > activities (A**4/AMU), depolarization ratios for plane and unpolarized > incident light, reduced masses (AMU), force constants (mDyne/A), > and normal coordinates: > 1 2 3 > A A A > Frequencies -- -2672.6281 525.4568 578.5686 > Red. masses -- 1.0263 22.2631 1.0304 > Frc consts -- 4.3194 3.6217 0.2032 > IR Inten -- 7645.8759 16.4800 57.7877 > Atom AN X Y Z X Y Z X Y Z > > 1 9 -0.02 -0.01 0.01 0.68 0.42 -0.34 -0.02 0.02 > -0.01 > 2 1 0.79 0.48 -0.38 0.14 -0.01 0.00 0.61 -0.65 > 0.45 > 3 17 -0.01 -0.01 0.01 -0.38 -0.23 0.18 -0.01 0.01 > -0.01 > > However, if I tried to start over to do a TS locating calculation using the > same theory/basis-level uhf/sto-3g opt(TS,calcall,noeigentest) nosymm as I > used in obtaining the stationary point and the freq calculation as above, > the job continued to run, seemingly to confirm the TS point found previously > was not the correct one. Could anyone please suggest what might go wrong > here? It is a very short run of g03; hope you can pleasea let me know what > you may get. > > Thanks a lot! > > > --00163692008ae136810496857e9a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Li,
=A0
Why did you use the noeigentest?=A0 If you do not allow the optimizer = to check if it is going to a saddle point or to a minimum, then the optimiz= ation will proceed in some direction.=A0 You may have asked for a TS, but s= ince the optimizer cannot determine where it is going, then you will probab= ly end up some place other than where you wanted.=A0
=A0
SOmething else... did you check the convergence criteria after the fre= quency calculation?=A0 Sometimes an optimization says it has reached a stat= ionary point, only to find out that the newly calculated=A0Hessian=A0says y= ou are still an optimization step or two away.=A0 And this would explain wh= y, in conjunction with the noeigentest, your optimization continues.
=A0
Hope this helps...
=A0
=A0
Mark=A0

I cannot totally say why you observe this, but
On Thu, Dec 2, 2010 at 10:49 PM, Li qiang cougar= head_2003||yahoo.com <= ;owner-chemistry__ccl.net>= wrote:
Hi CCL'ers:

I have a somewhat strange TS loca= ting problem wtih g03. My first run of locating the TS was completed fine, = with the output of the optimized TS coordinates:

=A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Input orientation: =A0 =A0 =A0 =A0 =A0 =A0= =A0 =A0 =A0 =A0 =A0 =A0 =A0
=A0--------------------------------------------------------------------- =A0Center =A0 =A0 Atomic =A0 =A0 Atomic =A0 =A0 =A0 =A0 =A0 =A0 =A0Coordi= nates (Angstroms)
=A0Number =A0 =A0 Number =A0 =A0 =A0Type =A0 =A0 =A0 = =A0 =A0 =A0 =A0X =A0 =A0 =A0 =A0 =A0 Y =A0 =A0 =A0 =A0 =A0 Z
=A0-------= --------------------------------------------------------------
=A0 =A0 1 =A0 =A0 =A0 =A0 =A09 =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -3.386= 882 =A0 =A01.262162 =A0 -0.189094
=A0 =A0 2 =A0 =A0 =A0 =A0 =A01 =A0 = =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -4.252089 =A0 =A00.740968 =A0 =A00.231843=
=A0 =A0 3 =A0 =A0 =A0 =A0 17 =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -5.= 482326 =A0 -0.002357 =A0 =A00.832002
=A0---------------------------------------------------------------------
because I saw the convergence in the optimization is:
=A0 =A0 =A0 = =A0=A0 Item =A0 =A0 =A0 =A0 =A0 =A0 =A0 Value =A0 =A0 Threshold =A0Converge= d?
=A0Maximum Force =A0 =A0 =A0 =A0 =A0 =A00.000032 =A0 =A0 0.000450 = =A0 =A0 YES
=A0RMS =A0 =A0 Force =A0 =A0 =A0 =A0 =A0 =A00.000022 =A0 =A0 0.000300 =A0 = =A0 YES
=A0Maximum Displacement =A0 =A0 0.000697 =A0 =A0 0.001800 =A0 = =A0 YES
=A0RMS =A0 =A0 Displacement =A0 =A0 0.000666 =A0 =A0 0.001200 = =A0 =A0 YES
=A0Predicted change in Energy=3D-1.988338D-08
=A0Optimization completed.
=A0 =A0 -- Stationary point found.

A= nd the link1 freq calculation shows:
Harmonic frequencies (cm**-1), IR i= ntensities (KM/Mole), Raman scattering
=A0activities (A**4/AMU), depola= rization ratios for plane and unpolarized
=A0incident light, reduced masses (AMU), force constants (mDyne/A),
=A0= and normal coordinates:
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A03
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0A =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0A =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0A
=A0Frequencies -- -2672.6281 =A0 =A0 =A0 =A0 =A0 =A0 =A0 525.4568 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 578.5686
=A0Red. masses -- =A0 =A0 1.0263 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A022.2631 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.0304
= =A0Frc consts =A0-- =A0 =A0 4.3194 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 3.6217 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.2032
=A0IR Inten =A0 =A0-- =A07645.8759 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A016.4800 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A057.7877
=A0Atom AN =A0 =A0 =A0X =A0 =A0 = =A0Y =A0 =A0 =A0Z =A0 =A0 =A0 =A0X =A0 =A0 =A0Y =A0 =A0 =A0Z =A0 =A0 =A0 = =A0X =A0 =A0 =A0Y =A0 =A0 =A0Z
=A0 =A01 =A0 9 =A0 =A0-0.02 =A0-0.01 =A0= 0.01 =A0 =A0 0.68 =A0 0.42 =A0-0.34 =A0 =A0-0.02 =A0 0.02 =A0-0.01
=A0 =A02 =A0 1 =A0 =A0 0.79 =A0 0.48 =A0-0.38 =A0 =A0 0.14 =A0-0.01 =A0 0.0= 0 =A0 =A0 0.61 =A0-0.65 =A0 0.45
=A0 =A03 =A017 =A0 =A0-0.01 =A0-0.01 = =A0 0.01 =A0 =A0-0.38 =A0-0.23 =A0 0.18 =A0 =A0-0.01 =A0 0.01 =A0-0.01
=
However, if I tried to start over to do a TS locating calculation using= the same theory/basis-level uhf/sto-3g opt(TS,calcall,noeigentest) nosymm = as I used in obtaining the stationary point and the freq calculation as abo= ve, the job continued to run, seemingly to confirm the TS point found previ= ously was not the correct one. Could anyone please suggest what might go wr= ong here? It is a very short run of g03; hope you can pleasea let me know w= hat you may get.

Thanks a lot!


<= br> --00163692008ae136810496857e9a-- From owner-chemistry@ccl.net Fri Dec 3 14:01:00 2010 From: "Jamin Krinsky krinsky.jamin%gmail.com" To: CCL Subject: CCL:G: regarding TDDFt Optimization in gaussian Message-Id: <-43277-101203132805-14038-60U7YHP2z7ushV1cMjn4eg!^!server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 3 Dec 2010 10:27:55 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [krinsky.jamin * gmail.com] Hi Anup, Your first example asks for an optimization of the second triplet excited state, T2, with a singlet ground state. The second example specifies a triplet ground state and asks for the first excited state, which on initial inspection should be the same calculation as the first example (note that the "triplets" option here is ignored because if you start with an open-shell system Gaussian will just calculate excited states of the same multiplicity). These are not actually the same calculation because in the second case you are applying the TD algorithm to a (presumably converged) unrestricted "wavefunction," so you will get a different answer (I would think that in a well-behaved system they should be similar). Using a singlet ground state should save you a lot of compute time because a restricted wavefunction is calculated much more quickly. But ultimately the one to choose is the one that gives better results... Jamin On Fri, Dec 3, 2010 at 1:57 AM, Anup Thomas anupiict .. gmail.com wrote: > > Sent to CCL by: "Anup  Thomas" [anupiict-,-gmail.com] > I, Anup Thomas, a newbie in computational chemistry. Please answer me ? > > > i would like to optimize the second Triplet state T2 using TDDFT > > but i am confused of keywords (my Seniors and i differ in some arguement) > > which one of the following is correct (Is there any differnce for these two approaches) > > > #p b3lyp/6-31G* Td(triplets,root=2) opt > > title > > 0 1 > geometry > >               or > > #p b3lyp/6-31G* Td(triplets,root=1) opt > > title > > 0 3 > geometry > > Look forward to hear from you all > > Thank you > Anup Thomas>      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> > > From owner-chemistry@ccl.net Fri Dec 3 14:58:00 2010 From: "William F. Coleman wcoleman ~~ wellesley.edu" To: CCL Subject: CCL:G: a question regarding TS finding in g03 Message-Id: <-43278-101203141355-12180-lh9FDXCUFRGoU9H75lzgPA~~server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--21dbe6ae.21dbe392.c91ef1eb" Date: Fri, 03 Dec 2010 14:13:47 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman###wellesley.edu] This is a multi-part message in MIME format. ----=_--21dbe6ae.21dbe392.c91ef1eb Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit "CCL Subscribers" writes: >However, my questions is: why the optimized transition state structure >obtained by one successful g03 run could not be confirmed in the second >g03 run when the final optimized structure was given as the input? To what are you trying to optimize in the second experiment? If the reaction is unimolecular then I would expect optimization to lead to the starting molecule in the first calculation. If you are optimizing to a TS it would seem that you are asking for a TS of the first TS, and that may not make sense. Perhaps I am misunderstanding the question. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html http://www.flicksstuff.com/photos/pictures.html new galleries 9/4/2010 Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--21dbe6ae.21dbe392.c91ef1eb Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
"CCL Subscribers" <chemistry=40ccl.net> writes:
However, my questions is: why the optimized transition state = structure obtained by one successful g03 run could not be confirmed in the = second g03 run when the final optimized structure was given as the input?

To what are you trying to optimize in= the second experiment?  If the reaction is unimolecular then I would = expect optimization to lead to the starting molecule in the first calculati= on.  If you are optimizing to a TS it would seem that you are asking f= or a TS of the first TS, and that may not make sense.

Perhaps I am misunderstanding the que= stion.

Cheers,

Flick

_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481


Editor, JCE WebWare and JCE Featured = Molecules


----=_--21dbe6ae.21dbe392.c91ef1eb-- From owner-chemistry@ccl.net Fri Dec 3 15:32:00 2010 From: "Jean Jules FIFEN julesfifen=gmail.com" To: CCL Subject: CCL:G: a question regarding TS finding in g03 Message-Id: <-43279-101203152016-18868-633auaaipBnBAot/a/kbMg[*]server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=0015175cb05eaf0c06049687436e Date: Fri, 3 Dec 2010 21:20:07 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen*gmail.com] --0015175cb05eaf0c06049687436e Content-Type: text/plain; charset=ISO-8859-1 Hi! It is generally normal that the optimization starts to diverge when starting it at (or very near of) the stationary point geometry. This is due to the optimization algorithm. You may have a tour there. On 3 December 2010 17:25, Li qiang cougarhead_2003#yahoo.com < owner-chemistry*ccl.net> wrote: > Hi Ivo, > > Thank you for your reply. But you probably did not answer the part I feel > puzzled. > > I know how to identify whether the transition state optimization in g03 > gets the imaginary freq and how to visualize it etc. and how to confirm the > whether it is related to the intended reaction by doing an IRC calculation. > > However, my questions is: why the optimized transition state structure > obtained by one successful g03 run could not be confirmed in the second g03 > run when the final optimized structure was given as the input? > > Thank you again and anyone who may post an answer. > > > --- On *Fri, 12/3/10, Ivo Jacobs jacobs.ivo!A!gmail.com > * wrote: > > > From: Ivo Jacobs jacobs.ivo!A!gmail.com > Subject: CCL:G: a question regarding TS finding in g03 > To: "Li, Qiang " > Date: Friday, December 3, 2010, 3:48 AM > > > Hello, > > I would say that you have definately found a transition state, but you > should make sure that it is indeed the transition state that you are > interested in. First of all you can visualise the negative vibration with > gausview to make sure that it corresponds to the right reaction coordinate. > Then to be absolutely sure you should do a IRC calculation to find the two > minima that are connected to this transition state. > > Good luck, > Ivo Jacobs > > > On 3-12-10 4:49 AM, Li qiang cougarhead_2003||yahoo.com wrote: > > Hi CCL'ers: > > I have a somewhat strange TS locating problem wtih g03. My first run of > locating the TS was completed fine, with the output of the optimized TS > coordinates: > > Input orientation: > --------------------------------------------------------------------- > Center Atomic Atomic Coordinates (Angstroms) > Number Number Type X Y Z > --------------------------------------------------------------------- > 1 9 0 -3.386882 1.262162 -0.189094 > 2 1 0 -4.252089 0.740968 0.231843 > 3 17 0 -5.482326 -0.002357 0.832002 > --------------------------------------------------------------------- > > because I saw the convergence in the optimization is: > Item Value Threshold Converged? > Maximum Force 0.000032 0.000450 YES > RMS Force 0.000022 0.000300 YES > Maximum Displacement 0.000697 0.001800 YES > RMS Displacement 0.000666 0.001200 YES > Predicted change in Energy=-1.988338D-08 > Optimization completed. > -- Stationary point found. > > And the link1 freq calculation shows: > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering > activities (A**4/AMU), depolarization ratios for plane and unpolarized > incident light, reduced masses (AMU), force constants (mDyne/A), > and normal coordinates: > 1 2 3 > A A A > Frequencies -- -2672.6281 525.4568 578.5686 > Red. masses -- 1.0263 22.2631 1.0304 > Frc consts -- 4.3194 3.6217 0.2032 > IR Inten -- 7645.8759 16.4800 57.7877 > Atom AN X Y Z X Y Z X Y Z > > 1 9 -0.02 -0.01 0.01 0.68 0.42 -0.34 -0.02 0.02 > -0.01 > 2 1 0.79 0.48 -0.38 0.14 -0.01 0.00 0.61 -0.65 > 0.45 > 3 17 -0.01 -0.01 0.01 -0.38 -0.23 0.18 -0.01 0.01 > -0.01 > > However, if I tried to start over to do a TS locating calculation using the > same theory/basis-level uhf/sto-3g opt(TS,calcall,noeigentest) nosymm as I > used in obtaining the stationary point and the freq calculation as above, > the job continued to run, seemingly to confirm the TS point found previously > was not the correct one. Could anyone please suggest what might go wrong > here? It is a very short run of g03; hope you can pleasea let me know what > you may get. > > Thanks a lot! > > > > > -- J. Jules. --0015175cb05eaf0c06049687436e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi!
It is generally normal that the optimization starts= to diverge when starting it at (or very near of) the stationary point geom= etry. This is due to the optimization algorithm. You may have a tour there.=

On 3 December 2010 17:25, Li qiang cougarhea= d_2003#yahoo.com <owner-chemistry*ccl.net> wrote:
Hi Ivo,

Thank you for your reply. But you probably did not answer th= e part I feel puzzled.

I know how to identify whether the transitio= n state optimization in g03 gets the imaginary freq and how to visualize it= etc. and how to confirm the whether it is related to the intended reaction= by doing an IRC calculation.

However, my questions is: why the optimized transition state structure = obtained by one successful g03 run could not be confirmed in the second g03= run when the final optimized structure was given as the input?

Thank you again and anyone who may post an answer.


--- On Fri= , 12/3/10, Ivo Jacobs jacobs.ivo!A!gmail.com <owner-chemistry-*-ccl.net> wrote:

From: Ivo Jacobs jacobs.ivo!A!gmail.com <owner-chemistry-*-ccl.net= >
Subject: CCL:G: a question regarding TS finding in g03
To: &= quot;Li, Qiang " <cougarhead_2003-*-yahoo.com>
Date: Friday, December 3, 2010, 3:48 AM

=20 =20 =20 Hello,

I would say that you have definately found a transition state, but you should make sure that it is indeed the transition state that you are interested in. First of all you can visualise the negative vibration with gausview to make sure that it corresponds to the right reaction coordinate. Then to be absolutely sure you should do a IRC calculation to find the two minima that are connected to this transition state.

Good luck,
Ivo Jacobs


On 3-12-10 4:49 AM, Li qiang cougarhead_2003||yahoo.com wrote:
Hi CCL'ers:

I have a somewhat strange TS locating problem wtih g03. My first run of locating the TS was completed fine, with the output of the optimized TS coordinates:

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Input ori= entation: =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0
=A0----------------------------------------------------------= -----------
=A0Center =A0 =A0 Atomic =A0 =A0 Atomic =A0 =A0 =A0 =A0 =A0 = =A0 =A0Coordinates (Angstroms)
=A0Number =A0 =A0 Number =A0 =A0 =A0Type =A0 =A0 =A0 =A0 =A0 = =A0 =A0X =A0 =A0 =A0 =A0 =A0 Y =A0 =A0 =A0 =A0 =A0 Z
=A0----------------------------------------------------------= -----------
=A0 =A0 1 =A0 =A0 =A0 =A0 =A09 =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 = =A0 =A0 -3.386882 =A0 =A01.262162 =A0 -0.189094
=A0 =A0 2 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 = =A0 =A0 -4.252089 =A0 =A00.740968 =A0 =A00.231843
=A0 =A0 3 =A0 =A0 =A0 =A0 17 =A0 =A0 =A0 =A0 =A0 =A0 0 =A0 = =A0 =A0 -5.482326 =A0 -0.002357 =A0 =A00.832002
=A0----------------------------------------------------------= -----------

because I saw the convergence in the optimization is:
=A0 =A0 =A0 =A0=A0 Item =A0 =A0 =A0 =A0 =A0 =A0 =A0 Value =A0= =A0 Threshold =A0Converged?
=A0Maximum Force =A0 =A0 =A0 =A0 =A0 =A00.000032 =A0 =A0 0.00= 0450 =A0 =A0 YES
=A0RMS =A0 =A0 Force =A0 =A0 =A0 =A0 =A0 =A00.000022 =A0 =A0 = 0.000300 =A0 =A0 YES
=A0Maximum Displacement =A0 =A0 0.000697 =A0 =A0 0.001800 =A0= =A0 YES
=A0RMS =A0 =A0 Displacement =A0 =A0 0.000666 =A0 =A0 0.001200= =A0 =A0 YES
=A0Predicted change in Energy=3D-1.988338D-08
=A0Optimization completed.
=A0 =A0 -- Stationary point found.

And the link1 freq calculation shows:
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
=A0activities (A**4/AMU), depolarization ratios for plane and unpolarized
=A0incident light, reduced masses (AMU), force constants (mDyne/A),
=A0and normal coordinates:
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A03
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0A =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0A =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0A
=A0Frequencies -- -2672.6281 =A0 =A0 =A0 =A0 =A0 =A0 =A0 525.= 4568 =A0 =A0 =A0 =A0 =A0 =A0 =A0 578.5686
=A0Red. masses -- =A0 =A0 1.0263 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A022.2631 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.0304
=A0Frc consts =A0-- =A0 =A0 4.3194 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 3.6217 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.2032
=A0IR Inten =A0 =A0-- =A07645.8759 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A016.4800 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A057.7877
=A0Atom AN =A0 =A0 =A0X =A0 =A0 =A0Y =A0 =A0 =A0Z =A0 =A0 =A0= =A0X =A0 =A0 =A0Y =A0 =A0 =A0Z =A0 =A0 =A0 =A0X =A0 =A0 =A0Y =A0 =A0 =A0Z
=A0 =A01 =A0 9 =A0 =A0-0.02 =A0-0.01 =A0 0.01 =A0 =A0 0.68 = =A0 0.42 =A0-0.34 =A0 =A0-0.02 =A0 0.02 =A0-0.01
=A0 =A02 =A0 1 =A0 =A0 0.79 =A0 0.48 =A0-0.38 =A0 =A0 0.14 = =A0-0.01 =A0 0.00 =A0 =A0 0.61 =A0-0.65 =A0 0.45
=A0 =A03 =A017 =A0 =A0-0.01 =A0-0.01 =A0 0.01 =A0 =A0-0.38 = =A0-0.23 =A0 0.18 =A0 =A0-0.01 =A0 0.01 =A0-0.01

However, if I tried to start over to do a TS locating calculation using the same theory/basis-level uhf/sto-3g opt(TS,calcall,noeigentest) nosymm as I used in obtaining the stationary point and the freq calculation as above, the job continued to run, seemingly to confirm the TS point found previously was not the correct one. Could anyone please suggest what might go wrong here? It is a very short run of g03; hope you can pleasea let me know what you may get.

Thanks a lot!


=20




--
= J. Jules.

--0015175cb05eaf0c06049687436e-- From owner-chemistry@ccl.net Fri Dec 3 16:15:00 2010 From: "Sayed Mesa elsayed.elmes#yahoo.com" To: CCL Subject: CCL:G: Is SMD/IEFPCM appropiate for charged transition metal complex? Message-Id: <-43280-101203145220-7543-UGDCcJVilowrepIFmAWPkQ-#-server.ccl.net> X-Original-From: "Sayed Mesa" Date: Fri, 3 Dec 2010 14:52:16 -0500 Sent to CCL by: "Sayed Mesa" [elsayed.elmes]*[yahoo.com] Dear CCL community; I want to study the thermochemistry of the following reaction in water using B3LYP/mixed basis set as implemented in Gaussian 09 : [Cu2L]4+ + OH- ----> [Cu2LOH]3+ Where [Cu2L]4+ is dinuclear copper complex. L is macrocyclic complex. I have two questions: 1- Is SMD/IEFPCM appropriate for charged transition metal complex? If not please let me know which solvation model is better? 2- Can I calculate Delta G and Delta H of this reaction using SMD/IEFPCM? N.B. I read that SMD the reommended choice for calculation the delta G of solavation http://www.gaussian.com/g_tech/g_ur/k_scrf.htm Thanks beforehand, Sayed