From owner-chemistry@ccl.net Tue Jul 1 03:11:00 2008 From: "VITORGE Pierre 094605 Pierre.VITORGE++cea.fr" To: CCL Subject: CCL:G: SCF is confused? Message-Id: <-37280-080701030908-30889-mduzJia++5+qMkC38qcFqA(-)server.ccl.net> X-Original-From: "VITORGE Pierre 094605" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 1 Jul 2008 09:08:53 +0200 MIME-Version: 1.0 Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE!^!cea.fr] Try a single point HF calculation, then your MP2 calculation with = Keyword guess=3Dread. If it does not work, you can try other = intermediary single point calculations with smaller basis set and poor = convergence in SCF options.=20 Pierre Vitorge =20 http://www.vitorge.name =20 -----Message d'origine----- De=A0: owner-chemistry]~[ccl.net [mailto:owner-chemistry]~[ccl.net]=20 Envoy=E9=A0: lundi 30 juin 2008 14:39 =C0=A0: VITORGE Pierre Objet=A0: CCL:G: SCF is confused? Sent to CCL by: "Sarah R Whittleton" [SWhittleton|dal.ca] Hi CCL, I am trying to run a BSSE single-point calculation (counterpoise) using = MP2 on an organotin compound. The tin atom is described using the = Stuttgart ECP and an augmented, triple-zeta basis set. After running = for 11 hours the calculation dies uncompleted and the output (copied = below) says that Density matrix is not changing but DIIS error and the = SCF is confused. I have run similar calculations with the same method = on different organotin compounds and this is the only one giving me = trouble. I want to keep the method (MP2) and basis set consistent = between compounds is there anything I can do to make resolve this = problem and allow the calculations to complete normally? I have also = included the first lines of the input file for this calculation. I thank you all in advance for any suggestions, Sarah Whittleton =09 ******************************** Ph.D. Candidate Department of Chemistry Dalhousie University Halifax, NS B3H 4J3 THE END OF THE OUTPUT FILE: The electronic state of the initial guess is 2-A. of initial guess=3D 0.7500 Requested convergence on RMS density matrix=3D1.00D-08 within 128 = cycles. Requested convergence on MAX density matrix=3D1.00D-06. Requested convergence on energy=3D1.00D-06. No special actions if energy rises. Restarting incremental Fock formation. Density matrix is not changing but DIIS error=3D 1.23D-06 = CofLast=3D-1.58D-02. The SCF is confused. Error termination via Lnk1e in /usr/local/gaussian/g03/l502.exe at Tue = Jun 24 22:30:03 2008. Job cpu time: 0 days 11 hours 8 minutes 18.9 seconds. File lengths (MBytes): RWF=3D 65118 Int=3D 0 D2E=3D 0 = Chk=3D 8 Scr=3D 1 THE INPUT FILE: %mem=3D2GB %nprocs=3D3 %chk=3DMP2-test.chk # MP2/GenECP Pseudo=3DRead counterpoise=3D2 maxdisk=3D200GB -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jul 1 12:45:01 2008 From: "veronica ferraresi veroferraresi*_*gmail.com" To: CCL Subject: CCL:G: SCF is confused? Message-Id: <-37281-080701080503-355-DQ/h3OYyXBx1lH4ngpi8kQ.:.server.ccl.net> X-Original-From: "veronica ferraresi" Content-Type: multipart/alternative; boundary="----=_Part_961_10440278.1214910121332" Date: Tue, 1 Jul 2008 08:02:01 -0300 MIME-Version: 1.0 Sent to CCL by: "veronica ferraresi" [veroferraresi^^gmail.com] ------=_Part_961_10440278.1214910121332 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, I couldn't solve that error with xqc or qc or adding cycles to the scf. I solved it requesting the second derivatives at every point (opt=calcall), but I was doing an optimization and you are doing single point calculations, you can try, it takes a while. Vero. 2008/6/30 McGaughey, Georgia B. georgia_mcgaughey*|*merck.com < owner-chemistry[#]ccl.net>: > > Sent to CCL by: "McGaughey, Georgia B." [georgia_mcgaughey{}merck.com] > Sarah, > > Have you tried any other key words? For calculating dimer interactions > using MP2/aug-cc-pvdz, I typically use the Counterpoise=2 keyword (in > Gaussian) along w/ SCF=(qc,tight,maxcycle=512). I too had "SCF is > confused" in my output on occasion prior to adding in the SCF syntax. > > -Georgia > > -----Original Message----- > > From: owner-chemistry_+_ccl.net [mailto:owner-chemistry_+_ccl.net > ] > Sent: Monday, June 30, 2008 8:39 AM > To: McGaughey, Georgia B. > Subject: CCL:G: SCF is confused? > > > Sent to CCL by: "Sarah R Whittleton" [SWhittleton|dal.ca] > Hi CCL, > > I am trying to run a BSSE single-point calculation (counterpoise) using > MP2 on an organotin compound. The tin atom is described using the > Stuttgart ECP and an augmented, triple-zeta basis set. After running > for 11 hours the calculation dies uncompleted and the output (copied > below) says that Density matrix is not changing but DIIS error and the > SCF is confused. I have run similar calculations with the same method > on different organotin compounds and this is the only one giving me > trouble. I want to keep the method (MP2) and basis set consistent > between compounds is there anything I can do to make resolve this > problem and allow the calculations to complete normally? I have also > included the first lines of the input file for this calculation. > > I thank you all in advance for any suggestions, > Sarah Whittleton > > ******************************** > Ph.D. Candidate > Department of Chemistry > Dalhousie University > Halifax, NS B3H 4J3 > > > THE END OF THE OUTPUT FILE: > The electronic state of the initial guess is 2-A. > of initial guess= 0.7500 > Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > No special actions if energy rises. > Restarting incremental Fock formation. > Density matrix is not changing but DIIS error= 1.23D-06 > CofLast=-1.58D-02. > The SCF is confused. > Error termination via Lnk1e in /usr/local/gaussian/g03/l502.exe at Tue > Jun 24 22:30:03 2008. > Job cpu time: 0 days 11 hours 8 minutes 18.9 seconds. > File lengths (MBytes): RWF= 65118 Int= 0 D2E= 0 Chk= 8 > Scr= 1 > > > THE INPUT FILE: > %mem=2GB > %nprocs=3 > %chk=MP2-test.chk > # MP2/GenECP Pseudo=Read counterpoise=2 maxdisk=200GBJob: > http://www.ccl.net/jobsNotice: This > e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates (which may be known > outside the United States as Merck Frosst, Merck Sharp & Dohme or > MSD and in Japan, as Banyu - direct contact information for affiliates is > available at http://www.merck.com/contact/contacts.html) that may be > confidential, proprietary copyrighted and/or legally privileged. It is > intended solely for the use of the individual or entity named on this > message. If you are not the intended recipient, and have received this > message in error, please notify us immediately by reply e-mail and > then delete it from your system. > > > > - This is automatically added to each message by the mailing script -> > > ------=_Part_961_10440278.1214910121332 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, I couldn't solve that error with xqc or qc or adding cycles to the scf. I solved it requesting the second derivatives at every point (opt=calcall), but I was doing an optimization and you are doing single point calculations, you can try, it takes a while.
Vero.

2008/6/30 McGaughey, Georgia B. georgia_mcgaughey*|*merck.com <owner-chemistry[#]ccl.net>:

Sent to CCL by: "McGaughey, Georgia B." [georgia_mcgaughey{}merck.com]
Sarah,

Have you tried any other key words?  For calculating dimer interactions
using MP2/aug-cc-pvdz, I typically use the Counterpoise=2 keyword (in
Gaussian) along w/ SCF=(qc,tight,maxcycle=512).  I too had "SCF is
confused" in my output on occasion prior to adding in the SCF syntax.

-Georgia

-----Original Message-----
> From: owner-chemistry_+_ccl.net [mailto:owner-chemistry_+_ccl.net]
Sent: Monday, June 30, 2008 8:39 AM
To: McGaughey, Georgia B.
Subject: CCL:G: SCF is confused?


Sent to CCL by: "Sarah R Whittleton" [SWhittleton|dal.ca]
Hi CCL,

I am trying to run a BSSE single-point calculation (counterpoise) using
MP2 on an organotin compound.  The tin atom is described using the
Stuttgart ECP and an augmented, triple-zeta basis set.  After running
for 11 hours the calculation dies uncompleted and the output (copied
below) says that Density matrix is not changing but DIIS error and the
SCF is confused.  I have run similar calculations with the same method
on different organotin compounds and this is the only one giving me
trouble.  I want to keep the method (MP2) and basis set consistent
between compounds  is there anything I can do to make resolve this
problem and allow the calculations to complete normally?  I have also
included the first lines of the input file for this calculation.

I thank you all in advance for any suggestions,
Sarah Whittleton

********************************
Ph.D. Candidate
Department of Chemistry
Dalhousie University
Halifax, NS  B3H 4J3


THE END OF THE OUTPUT FILE:
The electronic state of the initial guess is 2-A.
 <S**2> of initial guess= 0.7500
 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
 Requested convergence on MAX density matrix=1.00D-06.
 Requested convergence on             energy=1.00D-06.
 No special actions if energy rises.
 Restarting incremental Fock formation.
 Density matrix is not changing but DIIS error= 1.23D-06
CofLast=-1.58D-02.
 The SCF is confused.
 Error termination via Lnk1e in /usr/local/gaussian/g03/l502.exe at Tue
Jun 24 22:30:03 2008.
 Job cpu time:  0 days 11 hours  8 minutes 18.9 seconds.
 File lengths (MBytes):  RWF=  65118 Int=      0 D2E=      0 Chk=      8
Scr=      1


THE INPUT FILE:
%mem=2GB
%nprocs=3
%chk=MP2-test.chk
# MP2/GenECP Pseudo=Read counterpoise=2 maxdisk=200GB


http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe: Job: http://www.ccl.net/jobs http://www.ccl.net/spammers.txtNotice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates (which may be known
outside the United States as Merck Frosst, Merck Sharp & Dohme or
MSD and in Japan, as Banyu - direct contact information for affiliates is
available at http://www.merck.com/contact/contacts.html) that may be
confidential, proprietary copyrighted and/or legally privileged. It is
intended solely for the use of the individual or entity named on this
message. If you are not the intended recipient, and have received this
message in error, please notify us immediately by reply e-mail and
then delete it from your system.



- This is automatically added to each message by the mailing script -
E-mail to subscribers: CHEMISTRY[#]ccl.net or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST[#]ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/htdig  (login: ccl, Password: search)
     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



------=_Part_961_10440278.1214910121332-- From owner-chemistry@ccl.net Tue Jul 1 20:16:01 2008 From: "gnli gnli:-:dicp.ac.cn" To: CCL Subject: CCL:G: how to define a radical molecule in G03? Message-Id: <-37282-080701054152-8406-peO8DNXTfkuKFE3gubr40g]~[server.ccl.net> X-Original-From: "gnli" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0000_01C8DB9F.B4E504D0" Date: Tue, 1 Jul 2008 17:27:08 +0800 MIME-Version: 1.0 Sent to CCL by: "gnli" [gnli(_)dicp.ac.cn] This is a multi-part message in MIME format. ------=_NextPart_000_0000_01C8DB9F.B4E504D0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear CCLer, Now I need to calculate a radical reaction, but I don't know how to define the radical molecule in G03 input file, could you please give me some advice? A example of simple input file about radical molecule is very appreciated! best wishes Guanna Li gnli%x%dicp.ac.cn ------=_NextPart_000_0000_01C8DB9F.B4E504D0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = CCLer,

Now I need = to calculate a radical reaction, but I don’t know how to define the = radical molecule in G03 input file, could you please give me some advice? =

A example = of simple input file about radical molecule is very appreciated! =

best wishes
Guanna Li
gnli%x%dicp.ac.cn



 

------=_NextPart_000_0000_01C8DB9F.B4E504D0-- From owner-chemistry@ccl.net Tue Jul 1 21:07:00 2008 From: "Jan Green jangreen0|-|lycos.com" To: CCL Subject: CCL: QSAR of Oxidation Potential Message-Id: <-37283-080701151553-29070-sJYDay9mv51tSsD60s6f3Q%server.ccl.net> X-Original-From: "Jan Green" Date: Tue, 1 Jul 2008 15:15:49 -0400 Sent to CCL by: "Jan Green" [jangreen0{=}lycos.com] Hello there, Could someone update to me what is the current status of estimation oxidation potential of an organic molecule? Is there good correlation between HOMO/LOMO and oxidation potential? Many thanks, Jan From owner-chemistry@ccl.net Tue Jul 1 21:42:01 2008 From: "Jan Green jangreen0 ~ lycos.com" To: CCL Subject: CCL: Estimation of Oxidization Potential Message-Id: <-37284-080701161015-2636-Yg9fpY1MJl5eta30SqNE9g{:}server.ccl.net> X-Original-From: "Jan Green" Date: Tue, 1 Jul 2008 16:10:11 -0400 Sent to CCL by: "Jan Green" [jangreen0 : lycos.com] Hello there, Could someone update to me what is the current status of theoretical estimation of oxidation potential for set of small drug-like molecules? Is there a good correlation between oxidation potential and HOMO/LOMO, or other descriptors? Many thanks, Jan From owner-chemistry@ccl.net Tue Jul 1 22:17:00 2008 From: "Simon Halstead shalstead,hit.edu.cn" To: CCL Subject: CCL: MM3 forcefield Message-Id: <-37285-080701025545-29749-OUT/MN3pEjiQzPdF+i/wdA|-|server.ccl.net> X-Original-From: Simon Halstead Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 30 Jun 2008 22:55:32 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Simon Halstead [shalstead~!~hit.edu.cn] Dear all, I am trying to perform some simulations using the MM3 forcefield. However, I cannot find any explanation of the format of the forcefield. Could anyone please give me a brief description of the format of the forcefield (the form of the different terms and the various units too)? I already have all the different parameters, but unfortunately I only have access to journals that are available online. Thank you for your help, Simon Halstead From owner-chemistry@ccl.net Tue Jul 1 22:51:00 2008 From: "Christopher Cramer cramer . umn.edu" To: CCL Subject: CCL: QSAR of Oxidation Potential Message-Id: <-37286-080701221107-31068-dZicJb6kW+/gv2ZuyZk5qw]~[server.ccl.net> X-Original-From: Christopher Cramer Content-Type: multipart/alternative; boundary=Apple-Mail-1-434248555 Date: Tue, 1 Jul 2008 21:10:49 -0500 Mime-Version: 1.0 (Apple Message framework v926) Sent to CCL by: Christopher Cramer [cramer^^^umn.edu] --Apple-Mail-1-434248555 Content-Type: text/plain; charset=WINDOWS-1252; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable Jan, We have published a fair amount on this, and leading references include Winget, P.; Cramer, C. J.; Truhlar, D. G. =93Computation of Oxidation =20= and Reduction Potentials for Reversible and Dissociative Electron-=20 Transfer Reactions in Solution=94 Theor. Chem. Acc. 2004, 112, 217. Lewis, A.; Bumpus, J. A.; Truhlar, D. G.; Cramer, C. J. =93Molecular =20 Modeling of Environmentally Important Processes: Reduction =20 Potentials=94 J. Chem. Ed. 2004, 81, 596 (and erratum 2007, 84, 934) Other relevant quantum work includes Baik, M. H.; Friesner, R. A. "Computing redox potentials in solution: =20= Density functional theory as a tool for rational design of redox =20 agents" J. Phys. Chem. A 2002, 106, 7407. Fu, Y.; Liu, L.; Yu, H. Z.; Wang, Y. M.; Guo, Q. X. "Quantum-chemical =20= predictions of absolute standard redox potentials of diverse organic =20 molecules and free radicals in acetonitrile" J. Am. Chem. Soc. 2005, =20 127, 7227-7234. and, in the non-quantum arena Canonica, S.; Tratnyek, P. G. "Quantitative structure-activity =20 relationships for oxidation reactions of organic chemicals in water" =20 Environ. Toxicol. Chem. 2003, 22, 1743-1754. An early paper of ours that compared quantum predictions to more =20 physical-organicky approaches is Winget, P.; Weber, E. J.; Cramer, C. J.; Truhlar, D. G. "Computational =20= Electrochemistry: Aqueous One-Electron Oxidation Potentials for =20 Substituted Anilines" Phys. Chem. Chem. Phys. 2000, 2, 1231-1239. Best regards, Chris On Jul 1, 2008, at 2:15 PM, Jan Green jangreen0|-|lycos.com wrote: > > Sent to CCL by: "Jan Green" [jangreen0{=3D}lycos.com] > > Hello there, > > Could someone update to me what is the current status of estimation =20= > oxidation potential of an organic molecule? Is there good =20 > correlation between HOMO/LOMO and oxidation potential? > > Many thanks, > Jan > > -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 Mobile: (952) 297-2575 cramer|umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about the textbook "Essentials of Computational Chemistry: Theories and Models, 2nd Edition") --Apple-Mail-1-434248555 Content-Type: text/html; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable Jan,

We have = published a fair amount on this, and leading references = include

Winget, P.; Cramer, = C. J.; Truhlar, D. G. =93Computation of Oxidation and Reduction Potentials for Reversible and Dissociative Electron-Transfer Reactions in Solution=94 = Theor. Chem. Acc. = 2004, 112, = 217. 

Lewis, A.; Bumpus, = J. A.; Truhlar, D. G.; Cramer, C. J. =93Molecular Modeling of Environmentally = Important Processes:  Reduction = Potentials=94 J. Chem. Ed. 2004, 81, 596 (and erratum 2007, 84, = 934)

Other relevant quantum work = includes

Baik, M. H.; Friesner, R. A. = "Computing redox potentials in solution: Density functional theory as a = tool for rational design of redox agents" J. Phys. Chem. A = 2002, 106, 7407.

Fu, Y.; Liu, L.; Yu, H. = Z.; Wang, Y. M.; Guo, Q. X. "Quantum-chemical predictions of absolute = standard redox potentials of diverse organic molecules and free radicals = in acetonitrile" J. Am. Chem. Soc. 2005, 127, = 7227-7234.

and, in the non-quantum = arena

Canonica, S.; Tratnyek, P. G. = "Quantitative structure-activity relationships for oxidation reactions = of organic chemicals in water" Environ. Toxicol. Chem. = 2003, 22, 1743-1754.

An early = paper of ours that compared quantum predictions to more = physical-organicky approaches is

Phys. Chem. Chem. Phys. 2000, = 2, 1231-1239.


Best = regards,

Chris

On Jul 1, 2008, at 2:15 PM, Jan Green jangreen0|-|lycos.com = wrote:


Sent to CCL by: "Jan  Green" = [jangreen0{=3D}lycos.com]

Hello there,

Could someone = update to me what is the current status of estimation oxidation = potential of an organic molecule?  Is there good correlation = between HOMO/LOMO and oxidation potential?

Many = thanks,
Jan




Christopher J. Cramer

University of = Minnesota

207 Pleasant St. SE

Minneapolis, MN = 55455-0431

Phone:  (612) 624-0859 || = FAX:  (612) = 626-2006

cramer|umn.edu

http://pollux.chem.umn.edu/~cr= amer

    of Computational = Chemistry:  Theories and Models, = 2nd Edition")



=

= --Apple-Mail-1-434248555--