From owner-chemistry@ccl.net Tue Jan 25 02:30:00 2011 From: "luca bertini luca.bertini,+,unimib.it" To: CCL Subject: CCL: optimization of excited states Message-Id: <-43745-110125022923-13486-h65nYlogQQrtNsJG9qauQg(-)server.ccl.net> X-Original-From: "luca bertini" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1;format="flowed" Date: Tue, 25 Jan 2011 08:28:49 +0100 MIME-Version: 1.0 Sent to CCL by: "luca bertini" [luca.bertini]_[unimib.it] Hi there, the optimization the geometry of an excited state is not an easy task. In my experience, if in your system there are one or more transition metal atoms, the optimization can be very difficult to converge. Try first to use molecular symmetry, if any. Luca Bertini -- Luca Bertini Dipartimento di Biotecnologie e Bioscienze Universita' degli Studi di Milano-Bicocca Piazza della Scienza, 2 20126 Milano, Italy Tel: +39 02 64483438 email: luca.bertini|unimib.it On Mon, 24 Jan 2011 13:36:13 -0500 "Nick Isachenkov i.nick.|.mail.ru" wrote: > > Sent to CCL by: "Nick Isachenkov" [i.nick ~~ mail.ru] > I have a ticklish question. Recently I tried to optimize >first 3 excited states of molecules of interest. In >Foresman in 9 chapter there are some examples on how to >do it, but only under HF/CIS level of theory, so it >unaccebtible. When I try to do the same with DFT/TD level >my calculation drop down. Can you advise me. > > > > -= This is automatically added to each message by the >mailing script =- > To recover the email address of the author of the >message, please change > the strange characters on the top line to the | sign. >You can also> > E-mail to administrators: CHEMISTRY-REQUEST|ccl.net or >use> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: >http://www.ccl.net/chemistry/searchccl/index.shtml> > RTFI: >http://www.ccl.net/chemistry/aboutccl/instructions/ > > From owner-chemistry@ccl.net Tue Jan 25 04:41:01 2011 From: "Stan van Gisbergen vangisbergen-#-scm.com" To: CCL Subject: CCL: Energy Decomposition and reaction coordinate Message-Id: <-43746-110125044013-5647-oDhtiHHFVFS5E4ehgFog5Q ~ server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-633--186360066 Date: Tue, 25 Jan 2011 10:40:19 +0100 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Stan van Gisbergen [vangisbergen(_)scm.com] --Apple-Mail-633--186360066 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Dear Peter,=20 Perhaps the PyFrag tool may be of interest to you for this purpose:=20 http://www.few.vu.nl/~bickel/PyFrag.html It is described as follows:=20 The PyFrag program (released as PyFrag2007.01) is a "wrap-around" for = the Amsterdam Density Functional (ADF) package which facilitates routine = explorations and analyses (in terms of user-defined fragments) of one- = or multidimensional potential energy surfaces with the Amsterdam Density = Functional (ADF) package. PyFrag enables in particular a user-friendly = analysis of reaction paths in terms of the extended Activation Strain = model of chemical reactivity. Best regards, Stan On Jan 24, 2011, at 7:50 PM, P.D.Jarowski*|*surrey.ac.uk wrote: >=20 > Sent to CCL by: [P.D.Jarowski||surrey.ac.uk] > [Subject changed by CCL Moderator] >=20 > Dear all, >=20 > Is there a reliable method for doing energy decomposition analysis = along a reaction coordinate? I.e. for a reaction rather than a = intermolecular interaction. >=20 > Please let me know. >=20 > Best, >=20 > Peter >=20 > ***Sent via RoadSync=AE for Android=99 >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands =20 vangisbergen{}scm.com =20 http://www.scm.com T: +31-20-5987626 =20 F: +31-20-5987629 --Apple-Mail-633--186360066 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252 http://www.few.vu.nl/~bi= ckel/PyFrag.html

It is described as = follows:

The = PyFrag program (released as PyFrag2007.01) is a "wrap-around" for the = Amsterdam Density Functional (ADF) package which ADF) package. PyFrag enables in = particular a user-friendly analysis of reaction paths in terms of the = extended Activation Strain model of chemical = reactivity.

Best = regards,

Stan

On Jan 24, 2011, at 7:50 = PM, P.D.Jarowski*|*surrey.ac.uk wrote:

Sent to CCL by: = [P.D.Jarowski||surrey.ac.uk]
[Subject changed by CCL = Moderator]

Dear all,

Is there a reliable method for doing = energy decomposition analysis along a reaction coordinate? I.e. for a = reaction rather than a intermolecular interaction.

Please let me = know.

Best,

Peter

***Sent via RoadSync=AE for = Android=99

-=3D This is automatically added to each = message by the mailing script =3D-
To recover the email address of = the author of the message, please change
the strange characters on = the top line to the {} sign. You can also
look up the X-Original-From: = line in the mail header.

E-mail to subscribers: CHEMISTRY{}ccl.net = or use:
=      http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age

E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or = use
=      http://www.ccl.net/cgi-bin/ccl/send_ccl_mess= age
=      http://www.ccl.net/chemistry/sub_unsub.shtml=

Before posting, check wait time at: = http://www.ccl.net
Conferences: = http://server.ccl.net/chemistry/announcements/conferences/

Search = Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

If = your mail bounces from CCL with 5.7.1 error, check:
=      http://www.ccl.net/spammers.txt

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

Dr. S.J.A. van Gisbergen

Scientific Computing & Modelling NV

Theoretical Chemistry, Vrije Universiteit

De Boelelaan 1083

1081 HV = Amsterdam

The Netherlands = =

http://www.scm.com

T: +31-20-5987626

F: +31-20-5987629

= --Apple-Mail-633--186360066-- From owner-chemistry@ccl.net Tue Jan 25 05:47:00 2011 From: "Guilherme Luis Cordeiro guilhermecord*_*gmail.com" To: CCL Subject: CCL:G: Error on optimization Message-Id: <-43747-110125054630-10786-P36v8uIzw+zOfOhsGsMwOw###server.ccl.net> X-Original-From: "Guilherme Luis Cordeiro" Date: Tue, 25 Jan 2011 05:46:29 -0500 Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord^_^gmail.com] Hi Mr. Odon, I tried to do that optimization using Gaussian 98 in a Windows XP. Here is what how my output comes: %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. %chk=Q.chk Default route: MaxDisk=2000MB --------------------------- #T RHF/6-31+G(d,p) Opt Test --------------------------- open of exec.fil failed. Thanks. From owner-chemistry@ccl.net Tue Jan 25 07:30:01 2011 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas^-^chem.elte.hu" To: CCL Subject: CCL:G: Error on optimization Message-Id: <-43748-110125072530-19285-mFGd8PwUkLTO+5mrybmAcg===server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Tue, 25 Jan 2011 13:25:09 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas(0)chem.elte.hu] Hi, My guess is that the installation or starting was somewhat wrong, so the Gaussian directory is not in the search path, etc. How was it started, through GaussView or via the g98w executable? As there is no executable file system flag under the filesystems used in XP my guess is that the starting setup was incorrect. Here at that point l101.exe should be started. Is there a system administrator there who could look around what could be the problem? Please, rerun the job and put #P instead of # at the beginning of the command line. I might be able to help if send me the followings: How you start Gausssian The name of the directory where Gaussian 98 has been installed The contents of the file G98W.INI in this directory The full output file, it should not be too long. Best wishes, Odon Farkas Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Tuesday 25 January 2011 11:46:29 Guilherme Luis Cordeiro guilhermecord*_*gmail.com wrote: > Guilherme From owner-chemistry@ccl.net Tue Jan 25 08:54:00 2011 From: "Close, David M. CLOSED-,-mail.etsu.edu" To: CCL Subject: CCL:G: help with freq calculation Message-Id: <-43749-110125085157-4126-v6xXTkHzr5CdUy2eDZ1Kiw/./server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_9D6140C35ABD534F9C463F41FC3A9CC13E41CCFEetsums2etsuedu_" Date: Tue, 25 Jan 2011 13:51:40 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED,,mail.etsu.edu] --_000_9D6140C35ABD534F9C463F41FC3A9CC13E41CCFEetsums2etsuedu_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable CCL: I have performed a SCRF calculation in Gaussian and would like to have th= e thermodynamic properties. I tried a frequency calculation on the SCRF ca= lculation using the checkpoint file, with the line #b3lyp/6-31G(d) freq geo= m=3Dcheckpoint. This job started, read the proper geometry, and ran just u= ntil it was to start the frequency calculation. The last line printed was = Approx Polarizability, then failed with the line FiileIO operation on a non= -existent file. How do I get this to work? Regards, Dave Close --_000_9D6140C35ABD534F9C463F41FC3A9CC13E41CCFEetsums2etsuedu_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

CCL:<= /p>

I have performed a SCRF calculation in Gauss= ian and would like to have the thermodynamic properties. I tried a fr= equency calculation on the SCRF calculation using the checkpoint file, with= the line #b3lyp/6-31G(d) freq geom=3Dcheckpoint. This job started, r= ead the proper geometry, and ran just until it was to start the frequency c= alculation. The last line printed was Approx Polarizability, then fai= led with the line FiileIO operation on a non-existent file. How do I = get this to work?

Regards, Dave C= lose

= --_000_9D6140C35ABD534F9C463F41FC3A9CC13E41CCFEetsums2etsuedu_-- From owner-chemistry@ccl.net Tue Jan 25 10:01:00 2011 From: "andreas.goeller||bayer.com" To: CCL Subject: CCL: Antwort: CCL: Energy Decomposition and reaction coordinate Message-Id: <-43750-110125020116-32381-OPYBOhNxxiooABKVUCTQww.:.server.ccl.net> X-Original-From: andreas.goeller%bayer.com Content-Type: multipart/alternative; boundary="=_alternative 00268AC8C1257823_=" Date: Tue, 25 Jan 2011 08:00:59 +0100 MIME-Version: 1.0 Sent to CCL by: andreas.goeller#%#bayer.com Dies ist eine mehrteilige Nachricht im MIME-Format. --=_alternative 00268AC8C1257823_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Peter, have a look at recent publications by Bickelhaupt from Amsterdam=3D20 university. Freundliche Gr=FC=DFe / Best Regards Andreas Goeller --=_alternative 00268AC8C1257823_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Peter, have a look at recent publications by Bickelhaupt from Amsterdam=3D20 university.

Freundliche Gr=FC=DFe / Best Regards

Andreas Goeller

--=_alternative 00268AC8C1257823_=-- From owner-chemistry@ccl.net Tue Jan 25 10:35:00 2011 From: "Jim Kress ccl_nospam\a/kressworks.com" To: CCL Subject: CCL: Energy Decomposition and reaction coordinate Message-Id: <-43751-110124212503-10194-OrvLLQS/lI8RGDw/I2r21w|-|server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 24 Jan 2011 21:24:32 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam]|[kressworks.com] AOMix may allow you to do this. http://www.sg-chem.net/aomix/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com~~ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com~~ccl.net] On Behalf Of > P.D.Jarowski*|*surrey.ac.uk > Sent: Monday, January 24, 2011 1:51 PM > To: Kress, Jim > Subject: CCL: Energy Decomposition and reaction coordinate > > > Sent to CCL by: [P.D.Jarowski||surrey.ac.uk] > [Subject changed by CCL Moderator] > > Dear all, > > Is there a reliable method for doing energy decomposition analysis > along a reaction coordinate? I.e. for a reaction rather than a > intermolecular interaction. > > Please let me know. > > Best, > > Peter > > ***Sent via RoadSyncÂ® for Androidâ„¢> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Tue Jan 25 12:55:00 2011 From: "Guilherme Luis Cordeiro guilhermecord(0)gmail.com" To: CCL Subject: CCL:G: Error on optimization Message-Id: <-43752-110125101412-24017-5bfWgs+2+qaXZkfLGqB96A(~)server.ccl.net> X-Original-From: "Guilherme Luis Cordeiro" Date: Tue, 25 Jan 2011 10:14:10 -0500 Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord^_^gmail.com] Hi Mr. Farkas, I started Gaussian program through g98w executable. There are a couple of things I want to comment about: 1st) a message of error like: "Error message #2065 Can't overwrite/remove file C:\G98W\Scratch\gxx-exec.dat" 2nd) following the message above comes another like: "Severe error message #2070 The processing of the last link ended abnormally. All processing has been aborted." And the full output file is : Entering Link 1 = C:\G98W\l1.exe PID= 5844. Copyright (c) 1988,1990,1992,1993,1995,1998 Gaussian, Inc. All Rights Reserved. This is part of the Gaussian(R) 98 program. It is based on the Gaussian 94(TM) system (copyright 1995 Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992 Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990 Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988 Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986 Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983 Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under DFARS: RESTRICTED RIGHTS LEGEND Use, duplication or disclosure by the US Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraph (c) of the Commercial Computer Software - Restricted Rights clause at FAR 52.227-19. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 98, Revision A.9, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1998. ********************************************* Gaussian 98: x86-Win32-G98RevA.9 19-Apr-2000 25-Jan-2011 ********************************************* %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. %chk=Quer.chk Default route: MaxDisk=2000MB --------------------------- #P RHF/6-31+G(d,p) Opt Test --------------------------- 1/18=20,38=1/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,7=111,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,38=4/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7//1,2,3,16; 1/18=20/3(1); 99//99; 2/9=110/2; 3/5=1,6=6,7=111,11=1,25=1,30=1/1,2,3; 4/5=5,7=1,16=2/1; 5/5=2,38=4/2; 7//1,2,3,16; 1/18=20/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; Leave Link 1 at Tue Jan 25 12:07:57 2011, MaxMem= 6291456 cpu: 0.0 open of exec.fil failed. Thanks. From owner-chemistry@ccl.net Tue Jan 25 13:30:00 2011 From: "Jurgens Hendrik de Lange jurgensdl(a)gmail.com" To: CCL Subject: CCL:G: G09 RevB: Formalism for SCVS method - constant virial ratio Message-Id: <-43753-110125100032-1402-dkKKCHwse7Zb1LubFNK4KQ,,server.ccl.net> X-Original-From: "Jurgens Hendrik de Lange" Date: Tue, 25 Jan 2011 10:00:24 -0500 Sent to CCL by: "Jurgens Hendrik de Lange" [jurgensdl:+:gmail.com] Dear CCLers Can anybody tell me the formalism (keyword) in order to implement Todd Keith's Self-consistent virial scaling method in order to force the virial ratio to be exactly 2.00000, implemented in the newest Gaussian 09 revision? I have not found any reference to it in the G09 reference manual, though I suspect the online reference has not been updated to the newest revision. I believe it is not implemented automatically - I have several optimizations not adhering to the virial theorem. Thank you, Jurgens de Lange University of Pretoria, South Africa jurgensdl,+,tuks.co.za From owner-chemistry@ccl.net Tue Jan 25 14:05:00 2011 From: "Pietro Ottati pietro.ottati],[gmail.com" To: CCL Subject: CCL: Reaction simulation Qsite Message-Id: <-43754-110125102438-30649-gTmQsJXCbcQapX/NrBNBgg++server.ccl.net> X-Original-From: Pietro Ottati Content-Type: multipart/alternative; boundary=00151751142284fa7e049aad4f13 Date: Tue, 25 Jan 2011 16:24:20 +0100 MIME-Version: 1.0 Sent to CCL by: Pietro Ottati [pietro.ottati|gmail.com] --00151751142284fa7e049aad4f13 Content-Type: text/plain; charset=ISO-8859-1 Hi everybody, last time I asked you general question that wasn't clear. This time I hope that you can help me to find my street! I have to do this job to have my first scholarship, so I need to learn fast and good. I have to simulate all the reaction pathway of 3-HAO enzymes. http://pubs.acs.org/doi/abs/10.1021/bi047353l I have to simulate all step to understand the mechanism, (see page 7641 of the article). I'll try to find Transition state with Qsite in standard mode (not LST, not QST) The calculation run for 4-5 hours and in the end I obtain the same geometry that I started. No changes perfectly superimposed.... Is there somebody that use qsite and that can help me in my first steps in this new world? Tanks in advance. P.S. I read the manual of qsite, jaguar, etc... but don't help me in my everyday job. --00151751142284fa7e049aad4f13 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi everybody,

last time I asked you general question that wasn'= t clear. This time I hope that you can help me to find my street! I have to= do this job to have my first scholarship, so I need to learn fast and good= . I have to simulate all the reaction pathway of 3-HAO enzymes.

http://pubs.a= cs.org/doi/abs/10.1021/bi047353l

I have to simulate all step to = understand the mechanism, (see page 7641 of the article). I'll try to f= ind Transition state with Qsite in standard mode (not LST, not QST) The cal= culation run for 4-5 hours and in the end I obtain the same geometry that I= started. No changes perfectly superimposed....

Is there somebody that use qsite and that can help me in my first steps= in this new world?

Tanks in advance.

P.S. I read the manual = of qsite, jaguar, etc... but don't help me in my everyday job.

--00151751142284fa7e049aad4f13-- From owner-chemistry@ccl.net Tue Jan 25 14:40:00 2011 From: "Olegas Eicher-Lorka lorka!^!ktl.mii.lt" To: CCL Subject: CCL:G: help with freq calculation Message-Id: <-43755-110125110937-29237-giQin7GEz65XNRzxVM89Pg ~~ server.ccl.net> X-Original-From: "Olegas Eicher-Lorka" Content-Type: multipart/alternative; boundary="----=_NextPart_000_00AD_01CBBCBA.E15341E0" Date: Tue, 25 Jan 2011 18:08:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Olegas Eicher-Lorka" [lorka_+_ktl.mii.lt] This is a multi-part message in MIME format. ------=_NextPart_000_00AD_01CBBCBA.E15341E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dave: An example (SCRF freq calculation) is presented below: #p freq b3lyp/6-31G(d) scrf=3D(iefpcm,solvent=3D?) guess=3Dread = geom=3Dcheck=20 Regards, Olegas Eicher-Lorka CCL: I have performed a SCRF calculation in Gaussian and would like to = have the thermodynamic properties. I tried a frequency calculation on = the SCRF calculation using the checkpoint file, with the line = #b3lyp/6-31G(d) freq geom=3Dcheckpoint. This job started, read the = proper geometry, and ran just until it was to start the frequency = calculation. The last line printed was Approx Polarizability, then = failed with the line FiileIO operation on a non-existent file. How do I = get this to work? Regards, Dave Close __________ Information from ESET Smart Security, version of virus = signature database 5816 (20110125) __________ The message was checked by ESET Smart Security. http://www.eset.com ------=_NextPart_000_00AD_01CBBCBA.E15341E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dave:

An example (SCRF freq calculation) is presented below:

#p freq b3lyp/6-31G(d) = scrf=3D(iefpcm,solvent=3D?)=20 guess=3Dread geom=3Dcheck

Regards, Olegas = Eicher-Lorka

CCL:

I have performed a SCRF calculation in = Gaussian and=20 would like to have the thermodynamic properties. I tried a = frequency=20 calculation on the SCRF calculation using the checkpoint file, with = the line=20 #b3lyp/6-31G(d) freq geom=3Dcheckpoint. This job started, read = the proper=20 geometry, and ran just until it was to start the frequency = calculation. =20 The last line printed was Approx Polarizability, then failed with the = line=20 FiileIO operation on a non-existent file. How do I get this to=20 work?

Regards, Dave=20 Close

__________ Information from ESET = Smart=20 Security, version of virus signature database 5816 (20110125)=20 __________

The message was checked by ESET Smart = Security.

http://www.eset.com
------=_NextPart_000_00AD_01CBBCBA.E15341E0-- From owner-chemistry@ccl.net Tue Jan 25 15:14:00 2011 From: "P.D.Jarowski(a)surrey.ac.uk" To: CCL Subject: CCL:G: NBO analysis Message-Id: <-43756-110125134926-25931-ZdRZW+5ALqi1taBpviT/TQ|server.ccl.net> X-Original-From: Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Tue, 25 Jan 2011 18:49:07 +0000 MIME-Version: 1.0 Sent to CCL by: [P.D.Jarowski-.-surrey.ac.uk] Hello, I recently did an nbo analysis where I was looking for some donations into sigma star to rationalize some geometric bond elongations. I found the interactions in the second ordere perturbation analysis, but I have no idea how to assess whether or not they are significant. Does anyone know a rule of thumb for this? if the second order perturbations a re only a small percentage of the total energy then what amount of this is significant. I am getting numbers on the order of a few kcal/mol in a sea of interaction of similar magnitude. If you need the file, I could send it. Best, Peter ***Sent via RoadSync® for Android™ -----Original Message----- > From: VITORGE Pierre 094605 Pierre.VITORGE-,-cea.fr Sent: Jan 24, 2011 4:56 PM To: Jarowski PD Dr (Physics) Subject: CCL:G: NBO analysis Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE]![cea.fr] Marcin, I am simplifying your NBO output: 1. (1.99952) BD ( 1) C 1 - O 2 ( 28.51%) 0.5339* C 1 s( 24.94%)p 2.99( 74.66%) ( 71.49%) 0.8455* O 2 s( 39.85%)p 1.49( 59.48%) 2. (1.99959) BD ( 2) C 1 - O 2 ( 22.67%) 0.4761* C p86.96( 98.32%) ( 77.33%) 0.8794* O p54.81( 97.77%) 3. (2.00000) BD ( 3) C 1 - O 2 ( 22.41%) 0.4734* C p 1.00( 99.45%) ( 77.59%) 0.8809* O p 1.00( 99.56%) 6. (1.99926) LP ( 1) C 1 s( 76.76%)p 0.30( 23.20%) 7. (1.99335) LP ( 1) O 2 s( 58.46%)p 0.71( 41.47%) to highlight qualitative interpretation: NBOs 1, 2 and 3 are for C-O triple bond NBOs 2 and 3 are virtually 100% from p orbitals they certainly correspond to 2 pi bonds, if you further look elsewhere in the NBO output, you will certainly find that the p orbitals are px and py, since the C-O axis is usually taken as the z geometric axis, for symmetry reason probably one NBO with only px functions, the other NBO with only py functions NBO 1 is built from one C sp hydrid and one O sp hydrid. The p function should now be a pz one: this is the sigma bond. The interpretation of the % of s and p functions need to consider the LPs and the "second order perturbation analysis" of the NBO output, since NBO1 and the LPs are certainly of same symmetry, namely sigma. 6 and 7 are lone pairs (LPs), they certainly are of sigma symmetry as NBO 1, and as NBO 1 built with s and pz functions. For this reason they should not be interpreted independently from NBO 1. Do not hesitate to contact me directly (pierre.vitorge//\\cea.fr) for more details: Using Section Second order perturbation analysis Having a more quantitative interpretation directly from the MOs used by Gaussian (pop=full) -- Pierre Vitorge Directeur de recherche CEA Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, LAMBE, UMR 8587, CEA, Univ Evry, CNRS, Bd. Francois Mitterrand, Bat. Maupertuis, S 02 F-91025 Evry, France tel.01.69.47.01.40 (+33.1.69.47.01.40) http://www.lambe.univ-evry.fr/pvitorge http://www.vitorge.name Saclay : CEA, DEN, DPC, SECR, LSRM, Bat.391 Pe.121 F-91191 Gif-sur-Yvette, France. tel.01.69.08.32.65 (+33.1.69.08.32.65) -----Message d'origine----- De : owner-chemistry+pierre.vitorge==cea.fr() ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr() ccl.net] De la part de Marcin Sterniczuk m.sterniczuk,,ichtj.waw.pl Envoyé : lundi 24 janvier 2011 12:46 À : VITORGE Pierre 094605 Objet : CCL:G: NBO analysis Sent to CCL by: "Marcin Sterniczuk" [m.sterniczuk###ichtj.waw.pl] Hello, I have a problem with NBO analysis. How on +CO molecule example recognize hybrydization on carbon. What is hybrydization on orbital with unpaired electrone. One bonding orbital on carbon is sp3, two p and lone electron have orbital sp0,3. I know that sp0,3 we can describe sp. What we can do when some carbon centrum shows absurd like: one orbital sp3, one sp2, one sp and one p. That is a +CO part output from Gaussian 03W. (Occupancy) Bond orbital/ Coefficients/ Hybrids --------------------------------------------------------------------------------- 1. (1.99952) BD ( 1) C 1 - O 2 ( 28.51%) 0.5339* C 1 s( 24.94%)p 2.99( 74.66%)d 0.02( 0.39%) 0.0000 0.4639 -0.1850 0.7795 -0.0509 0.3691 -0.0133 0.0000 0.0000 0.0347 0.0000 0.0000 0.0425 -0.0304 ( 71.49%) 0.8455* O 2 s( 39.85%)p 1.49( 59.48%)d 0.02( 0.67%) 0.0000 0.6298 -0.0434 -0.7688 0.0247 0.0556 0.0059 0.0000 0.0000 0.0144 0.0000 0.0000 0.0697 -0.0403 2. (1.99959) BD ( 2) C 1 - O 2 ( 22.67%) 0.4761* C 1 s( 1.13%)p86.96( 98.32%)d 0.48( 0.55%) 0.0000 -0.0988 0.0394 -0.3676 0.0137 0.9208 -0.0114 0.0000 0.0000 0.0627 0.0000 0.0000 -0.0385 0.0065 ( 77.33%) 0.8794* O 2 s( 1.78%)p54.81( 97.77%)d 0.25( 0.45%) 0.0000 -0.1332 0.0092 -0.0390 -0.0061 0.9880 0.0032 0.0000 0.0000 -0.0656 0.0000 0.0000 0.0116 0.0085 3. (2.00000) BD ( 3) C 1 - O 2 ( 22.41%) 0.4734* C 1 s( 0.00%)p 1.00( 99.45%)d 0.01( 0.55%) 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9971 -0.0142 0.0000 0.0729 0.0147 0.0000 0.0000 ( 77.59%) 0.8809* O 2 s( 0.00%)p 1.00( 99.56%)d 0.00( 0.44%) 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.9978 0.0045 0.0000 -0.0651 -0.0131 0.0000 0.0000 4. (1.99981) CR ( 1) C 1 s(100.00%) 1.0000 0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 5. (1.99988) CR ( 1) O 2 s(100.00%)p 0.00( 0.00%) 1.0000 -0.0001 0.0000 -0.0001 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 6. (1.99926) LP ( 1) C 1 s( 76.76%)p 0.30( 23.20%)d 0.00( 0.03%) -0.0001 0.8757 0.0292 -0.4705 -0.0394 -0.0949 -0.0080 0.0000 0.0000 -0.0060 0.0000 0.0000 -0.0143 0.0089 7. (1.99335) LP ( 1) O 2 s( 58.46%)p 0.71( 41.47%)d 0.00( 0.07%) 0.0002 0.7641 0.0267 0.6311 0.0108 0.1273 0.0022 0.0000 0.0000 -0.0091 0.0000 0.0000 -0.0216 0.0135 8. (0.00673) RY*( 1) C 1 s( 64.49%)p 0.55( 35.30%)d 0.00( 0.21%) 0.0000 0.0883 0.7982 0.1569 0.5609 0.0317 0.1132 0.0000 0.0000 0.0154 0.0000 0.0000 0.0367 -0.0230 9. (0.00005) RY*( 2) C 1 s( 21.74%)p 2.25( 48.95%)d 1.35( 29.31%) 10. (0.00000) RY*( 3) C 1 s( 0.01%)p 1.00( 99.79%)d 0.00( 0.20%) 11. (0.00000) RY*( 4) C 1 s( 0.00%)p 1.00(100.00%)d 0.00( 0.00%) 12. (0.00000) RY*( 5) C 1 s( 1.37%)p 2.07( 2.83%)d70.09( 95.80%) 13. (0.00000) RY*( 6) C 1 s( 0.00%)p 1.00( 0.53%)d99.99( 99.47%) 14. (0.00000) RY*( 7) C 1 s( 0.00%)p 1.00( 0.02%)d99.99( 99.98%) 15. (0.00000) RY*( 8) C 1 s( 6.16%)p 1.75( 10.81%)d13.48( 83.03%) 16. (0.00000) RY*( 9) C 1 s( 3.40%)p 1.80( 6.13%)d26.63( 90.47%) 17. (0.00089) RY*( 1) O 2 s( 8.59%)p 4.64( 39.84%)d 6.00( 51.56%) 0.0000 0.0416 0.2902 -0.0794 -0.6136 -0.0160 -0.1238**************** -0.2411 **************** -0.5732 0.3590 18. (0.00003) RY*( 2) O 2 s( 11.89%)p 3.41( 40.51%)d 4.00( 47.61%) 19. (0.00000) RY*( 3) O 2 s( 0.57%)p99.99( 98.63%)d 1.41( 0.80%) 20. (0.00000) RY*( 4) O 2 s( 0.00%)p 1.00(100.00%)d 0.00( 0.00%) 21. (0.00000) RY*( 5) O 2 s( 0.00%)p 1.00( 0.98%)d99.99( 99.01%) 22. (0.00000) RY*( 6) O 2 s( 0.00%)p 1.00( 0.42%)d99.99( 99.58%) 23. (0.00000) RY*( 7) O 2 s( 0.00%)p 1.00( 0.02%)d99.99( 99.98%) 24. (0.00000) RY*( 8) O 2 s( 78.85%)p 0.27( 21.07%)d 0.00( 0.08%) 25. (0.00000) RY*( 9) O 2 s( 0.00%)p 1.00( 0.26%)d99.99( 99.74%) 26. (0.00041) BD*( 1) C 1 - O 2 ( 71.49%) 0.8455* C 1 s( 24.94%)p 2.99( 74.66%)d 0.02( 0.39%) 0.0000 0.4639 -0.1850 0.7795 -0.0509 0.3691 -0.0133 0.0000 0.0000 0.0347 0.0000 0.0000 0.0425 -0.0304 ( 28.51%) -0.5339* O 2 s( 39.85%)p 1.49( 59.48%)d 0.02( 0.67%) 0.0000 0.6298 -0.0434 -0.7688 0.0247 0.0556 0.0059 0.0000 0.0000 0.0144 0.0000 0.0000 0.0697 -0.0403 27. (0.00048) BD*( 2) C 1 - O 2 ( 77.33%) 0.8794* C 1 s( 1.13%)p86.96( 98.32%)d 0.48( 0.55%) 0.0000 -0.0988 0.0394 -0.3676 0.0137 0.9208 -0.0114 0.0000 0.0000 0.0627 0.0000 0.0000 -0.0385 0.0065 ( 22.67%) -0.4761* O 2 s( 1.78%)p54.81( 97.77%)d 0.25( 0.45%) 0.0000 -0.1332 0.0092 -0.0390 -0.0061 0.9880 0.0032 0.0000 0.0000 -0.0656 0.0000 0.0000 0.0116 0.0085 28. (0.00000) BD*( 3) C 1 - O 2 ( 77.59%) 0.8809* C 1 s( 0.00%)p 1.00( 99.45%)d 0.01( 0.55%) ( 22.41%) -0.4734* O 2 s( 0.00%)p 1.00( 99.56%)d 0.00( 0.44%) Thank youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://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 Tue Jan 25 15:50:00 2011 From: "Tijesunimi John Odebode tijesunimi=yahoo.com" To: CCL Subject: CCL:G: Gaussian question Message-Id: <-43757-110125144213-24569-OaNUsghC+lbx22azQCy8RQ^-^server.ccl.net> X-Original-From: "Tijesunimi John Odebode" Date: Tue, 25 Jan 2011 14:42:11 -0500 Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi:-:yahoo.com] Hello all, I was wondering if I could get an answer to this question: I did a geometry optimization of a compound using Gaussian(b3lyp/6-31G(d)). I found the HOMO and LUMO energy and calculated the energy gap. I then decided to do an MP2 single point calculation on the same compound to determine the HOMO and LUMO energy gap. The energy gap for the single point MP2 calculation was 3.49eV more than that for the b3lyp. Is this normal? Or do you think there is a problem somewhere? Has anybody carried out such calculations? Thanks a lot for your anticipated response. From owner-chemistry@ccl.net Tue Jan 25 16:25:00 2011 From: "Close, David M. CLOSED---mail.etsu.edu" To: CCL Subject: CCL:G: Error on optimization Message-Id: <-43758-110125142226-3923-+6dIZnIywd82lAI0YKX35A-,-server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 25 Jan 2011 19:21:42 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED|mail.etsu.edu] Guilherme: This is helpful to know. You are at least in Link1. And the program has read some of your input data and made a list of the subroutines it is going to call. The very next line to print is the job name. This is missing in the printout. Next comes the z-matrix. This too is missing. Without seeing your input file I would guess that either you don't have a job name on a single line, or you don't have a blank line before and after the job name. If these were properly listed, then there may be something wrong with the atom coordinates. After listing all the coordinates, you need a blank line. If none of this helps, send the input file. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu^_^ccl.net [mailto:owner-chemistry+closed==etsu.edu^_^ccl.net] On Behalf Of Guilherme Luis Cordeiro guilhermecord(0)gmail.com Sent: Tuesday, January 25, 2011 10:14 AM To: Close, David M. Subject: CCL:G: Error on optimization Sent to CCL by: "Guilherme Luis Cordeiro" [guilhermecord^_^gmail.com] Hi Mr. Farkas, I started Gaussian program through g98w executable. There are a couple of things I want to comment about: 1st) a message of error like: "Error message #2065 Can't overwrite/remove file C:\G98W\Scratch\gxx-exec.dat" 2nd) following the message above comes another like: "Severe error message #2070 The processing of the last link ended abnormally. All processing has been aborted." And the full output file is : Entering Link 1 = C:\G98W\l1.exe PID= 5844. Copyright (c) 1988,1990,1992,1993,1995,1998 Gaussian, Inc. All Rights Reserved. This is part of the Gaussian(R) 98 program. It is based on the Gaussian 94(TM) system (copyright 1995 Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992 Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990 Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988 Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986 Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983 Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under DFARS: RESTRICTED RIGHTS LEGEND Use, duplication or disclosure by the US Government is subject to restrictions as set forth in subparagraph (c)(1)(ii) of the Rights in Technical Data and Computer Software clause at DFARS 252.227-7013. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraph (c) of the Commercial Computer Software - Restricted Rights clause at FAR 52.227-19. Gaussian, Inc. Carnegie Office Park, Building 6, Pittsburgh, PA 15106 USA --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 98, Revision A.9, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 1998. ********************************************* Gaussian 98: x86-Win32-G98RevA.9 19-Apr-2000 25-Jan-2011 ********************************************* %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. %chk=Quer.chk Default route: MaxDisk=2000MB --------------------------- #P RHF/6-31+G(d,p) Opt Test --------------------------- 1/18=20,38=1/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,7=111,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,38=4/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7//1,2,3,16; 1/18=20/3(1); 99//99; 2/9=110/2; 3/5=1,6=6,7=111,11=1,25=1,30=1/1,2,3; 4/5=5,7=1,16=2/1; 5/5=2,38=4/2; 7//1,2,3,16; 1/18=20/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; Leave Link 1 at Tue Jan 25 12:07:57 2011, MaxMem= 6291456 cpu: 0.0 open of exec.fil failed. Thanks.http://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 Tue Jan 25 17:00:00 2011 From: "Tijesunimi John Odebode tijesunimi__yahoo.com" To: CCL Subject: CCL:G: Gaussian Error Message-Id: <-43759-110125142612-7353-3vaqPnbq5WNCZfQkWGszWA!=!server.ccl.net> X-Original-From: "Tijesunimi John Odebode" Date: Tue, 25 Jan 2011 14:26:10 -0500 Sent to CCL by: "Tijesunimi John Odebode" [tijesunimi+*+yahoo.com] Hello, I was wondering if anybody had an answer to my question. I am trying to visualize the HOMO and LUMO of a compound on MOLDEN of which I ran gaussian calculations on. I read an article online that says that for MOLDEN to find all required information in the output file, I need to run a single point calculation at the desired level of theory including the pop=full and gfinput keywords. I entered the above in my input file and the following is my input: %chk=Chlorin-1_b3lyp_go %mem=23000mb %nprocshared=8 # b3lyp/6-31G(d) sp scf=tight pop=full gfinput maxdisk=50gb b3lyp geometry optimization using Gaussian Chlorin-sp-1 The mem value in the run script is 23500mb and maxdisk=50gb. However, when I run this job, an error message comes up which says: galloc: cannot allocate memory. I tried increasing the memory on the run script to 24000mb but I keep getting the message Requested node configuration unavailable. I also tried leaving the memory on the run script as 23500mb and reducing the %mem on the input file to 20000mb; however, I keep getting the same message saying galloc: cannot allocate memory.' I do not know what the problem is. Is there a problem with my input file or what else do you think I should do. I am sorry if I did not do a good job explaining the problem; I am new to this. Thanks a lot for your anticipated response. Tijesunimi Odebode From owner-chemistry@ccl.net Tue Jan 25 23:02:00 2011 From: "Jamin Krinsky krinsky.jamin_+_gmail.com" To: CCL Subject: CCL:G: NBO analysis Message-Id: <-43760-110125230042-31730-0sEyjj/EU0Is84zfAmI13w##server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Tue, 25 Jan 2011 20:00:23 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [krinsky.jamin a gmail.com] Hi Peter, The perturbation analysis is indeed a little ambiguous. I would suggest requesting an NLMO analysis (I know you get this if you use the NBO keyword "dipole" but you probably can also just specify "nlmo", for example $NBO DIPOLE $END). This will give you a section of output with the delocalizations in terms of % of electrons in an NBO donated to another, which I have found much more instructive. Regards, Jamin On Tue, Jan 25, 2011 at 10:49 AM, P.D.Jarowski(a)surrey.ac.uk wrote: > > Sent to CCL by: [P.D.Jarowski-.-surrey.ac.uk] > > > Hello, I recently did an nbo analysis where I was looking for some donations into sigma star to rationalize some geometric bond elongations. I found the interactions in the second ordere perturbation analysis, but I have no idea how to assess whether or not they are significant. Does anyone know a rule of thumb for this? if the second order perturbations a re only a small percentage of the total energy then what amount of this is significant. I am getting numbers on the order of a few kcal/mol in a sea of interaction of similar magnitude. If you need the file, I could send it. > > Best, > > Peter > > ***Sent via RoadSync® for Android™ > > -----Original Message----- >> From: VITORGE Pierre 094605 Pierre.VITORGE-,-cea.fr > Sent: Jan 24, 2011 4:56 PM > To: Jarowski PD Dr (Physics) > Subject: CCL:G: NBO analysis > > > > > Sent to CCL by: "VITORGE Pierre 094605" [Pierre.VITORGE]![cea.fr] > Marcin, > > I am simplifying your NBO output: > > 1. (1.99952) BD ( 1) C 1 - O 2 > ( 28.51%) 0.5339* C 1 s( 24.94%)p 2.99( 74.66%) > ( 71.49%) 0.8455* O 2 s( 39.85%)p 1.49( 59.48%) > 2. (1.99959) BD ( 2) C 1 - O 2 > ( 22.67%) 0.4761* C p86.96( 98.32%) > ( 77.33%) 0.8794* O p54.81( 97.77%) > 3. (2.00000) BD ( 3) C 1 - O 2 > ( 22.41%) 0.4734* C p 1.00( 99.45%) > ( 77.59%) 0.8809* O p 1.00( 99.56%) > 6. (1.99926) LP ( 1) C 1 s( 76.76%)p 0.30( 23.20%) > 7. (1.99335) LP ( 1) O 2 s( 58.46%)p 0.71( 41.47%) > > to highlight qualitative interpretation: > > NBOs 1, 2 and 3 are for C-O triple bond > > NBOs 2 and 3 are virtually 100% from p orbitals they certainly correspond to 2 pi bonds, if you further look elsewhere in the NBO output, you will certainly find that the p orbitals are px and py, since the C-O axis is usually taken as the z geometric axis, for symmetry reason probably one NBO with only px functions, the other NBO with only py functions > > NBO 1 is built from one C sp hydrid and one O sp hydrid. The p function should now be a pz one: this is the sigma bond. The interpretation of the % of s and p functions need to consider the LPs and the "second order perturbation analysis" of the NBO output, since NBO1 and the LPs are certainly of same symmetry, namely sigma. > > 6 and 7 are lone pairs (LPs), they certainly are of sigma symmetry as NBO 1, and as NBO 1 built with s and pz functions. For this reason they should not be interpreted independently from NBO 1. > > Do not hesitate to contact me directly (pierre.vitorge//\\cea.fr) for more details: > > Using Section Second order perturbation analysis > > Having a more quantitative interpretation directly from the MOs used by Gaussian (pop=full) > > > > > > -- > Pierre Vitorge > Directeur de recherche CEA > > Laboratoire Analyse et Modelisation pour la Biologie et l Environnement, LAMBE, > UMR 8587, CEA, Univ Evry, CNRS, > Bd. Francois Mitterrand, Bat. Maupertuis, S 02 > F-91025 Evry, France > tel.01.69.47.01.40 (+33.1.69.47.01.40) > http://www.lambe.univ-evry.fr/pvitorge > http://www.vitorge.name > > Saclay : > CEA, DEN, DPC, SECR, LSRM, Bat.391 Pe.121 > F-91191 Gif-sur-Yvette, France. > tel.01.69.08.32.65 (+33.1.69.08.32.65) > > > -----Message d'origine----- > De : owner-chemistry+pierre.vitorge==cea.fr() ccl.net [mailto:owner-chemistry+pierre.vitorge==cea.fr() ccl.net] De la part de Marcin Sterniczuk m.sterniczuk,,ichtj.waw.pl > Envoyé : lundi 24 janvier 2011 12:46 > À : VITORGE Pierre 094605 > Objet : CCL:G: NBO analysis > > > Sent to CCL by: "Marcin Sterniczuk" [m.sterniczuk###ichtj.waw.pl] > Hello, > I have a problem with NBO analysis. How on +CO molecule example recognize hybrydization on carbon. What is hybrydization on orbital with unpaired electrone. One bonding orbital on carbon is sp3, two p and lone electron have orbital sp0,3. I know that sp0,3 we can describe sp. What we can do when some carbon centrum shows absurd like: one orbital sp3, one sp2, one sp and one p. That is a +CO part output from Gaussian 03W. > > (Occupancy) Bond orbital/ Coefficients/ Hybrids > --------------------------------------------------------------------------------- > 1. (1.99952) BD ( 1) C 1 - O 2 > ( 28.51%) 0.5339* C 1 s( 24.94%)p 2.99( 74.66%)d 0.02( 0.39%) > 0.0000 0.4639 -0.1850 0.7795 -0.0509 > 0.3691 -0.0133 0.0000 0.0000 0.0347 > 0.0000 0.0000 0.0425 -0.0304 > ( 71.49%) 0.8455* O 2 s( 39.85%)p 1.49( 59.48%)d 0.02( 0.67%) > 0.0000 0.6298 -0.0434 -0.7688 0.0247 > 0.0556 0.0059 0.0000 0.0000 0.0144 > 0.0000 0.0000 0.0697 -0.0403 > 2. (1.99959) BD ( 2) C 1 - O 2 > ( 22.67%) 0.4761* C 1 s( 1.13%)p86.96( 98.32%)d 0.48( 0.55%) > 0.0000 -0.0988 0.0394 -0.3676 0.0137 > 0.9208 -0.0114 0.0000 0.0000 0.0627 > 0.0000 0.0000 -0.0385 0.0065 > ( 77.33%) 0.8794* O 2 s( 1.78%)p54.81( 97.77%)d 0.25( 0.45%) > 0.0000 -0.1332 0.0092 -0.0390 -0.0061 > 0.9880 0.0032 0.0000 0.0000 -0.0656 > 0.0000 0.0000 0.0116 0.0085 > 3. (2.00000) BD ( 3) C 1 - O 2 > ( 22.41%) 0.4734* C 1 s( 0.00%)p 1.00( 99.45%)d 0.01( 0.55%) > 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.9971 -0.0142 0.0000 > 0.0729 0.0147 0.0000 0.0000 > ( 77.59%) 0.8809* O 2 s( 0.00%)p 1.00( 99.56%)d 0.00( 0.44%) > 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.9978 0.0045 0.0000 > -0.0651 -0.0131 0.0000 0.0000 > 4. (1.99981) CR ( 1) C 1 s(100.00%) > 1.0000 0.0001 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 0.0000 > 5. (1.99988) CR ( 1) O 2 s(100.00%)p 0.00( 0.00%) > 1.0000 -0.0001 0.0000 -0.0001 0.0000 > 0.0000 0.0000 0.0000 0.0000 0.0000 > 0.0000 0.0000 0.0000 0.0000 > 6. (1.99926) LP ( 1) C 1 s( 76.76%)p 0.30( 23.20%)d 0.00( 0.03%) > -0.0001 0.8757 0.0292 -0.4705 -0.0394 > -0.0949 -0.0080 0.0000 0.0000 -0.0060 > 0.0000 0.0000 -0.0143 0.0089 > 7. (1.99335) LP ( 1) O 2 s( 58.46%)p 0.71( 41.47%)d 0.00( 0.07%) > 0.0002 0.7641 0.0267 0.6311 0.0108 > 0.1273 0.0022 0.0000 0.0000 -0.0091 > 0.0000 0.0000 -0.0216 0.0135 > 8. (0.00673) RY*( 1) C 1 s( 64.49%)p 0.55( 35.30%)d 0.00( 0.21%) > 0.0000 0.0883 0.7982 0.1569 0.5609 > 0.0317 0.1132 0.0000 0.0000 0.0154 > 0.0000 0.0000 0.0367 -0.0230 > 9. (0.00005) RY*( 2) C 1 s( 21.74%)p 2.25( 48.95%)d 1.35( 29.31%) > 10. (0.00000) RY*( 3) C 1 s( 0.01%)p 1.00( 99.79%)d 0.00( 0.20%) > 11. (0.00000) RY*( 4) C 1 s( 0.00%)p 1.00(100.00%)d 0.00( 0.00%) > 12. (0.00000) RY*( 5) C 1 s( 1.37%)p 2.07( 2.83%)d70.09( 95.80%) > 13. (0.00000) RY*( 6) C 1 s( 0.00%)p 1.00( 0.53%)d99.99( 99.47%) > 14. (0.00000) RY*( 7) C 1 s( 0.00%)p 1.00( 0.02%)d99.99( 99.98%) > 15. (0.00000) RY*( 8) C 1 s( 6.16%)p 1.75( 10.81%)d13.48( 83.03%) > 16. (0.00000) RY*( 9) C 1 s( 3.40%)p 1.80( 6.13%)d26.63( 90.47%) > 17. (0.00089) RY*( 1) O 2 s( 8.59%)p 4.64( 39.84%)d 6.00( 51.56%) > 0.0000 0.0416 0.2902 -0.0794 -0.6136 > -0.0160 -0.1238**************** -0.2411 > **************** -0.5732 0.3590 > 18. (0.00003) RY*( 2) O 2 s( 11.89%)p 3.41( 40.51%)d 4.00( 47.61%) > 19. (0.00000) RY*( 3) O 2 s( 0.57%)p99.99( 98.63%)d 1.41( 0.80%) > 20. (0.00000) RY*( 4) O 2 s( 0.00%)p 1.00(100.00%)d 0.00( 0.00%) > 21. (0.00000) RY*( 5) O 2 s( 0.00%)p 1.00( 0.98%)d99.99( 99.01%) > 22. (0.00000) RY*( 6) O 2 s( 0.00%)p 1.00( 0.42%)d99.99( 99.58%) > 23. (0.00000) RY*( 7) O 2 s( 0.00%)p 1.00( 0.02%)d99.99( 99.98%) > 24. (0.00000) RY*( 8) O 2 s( 78.85%)p 0.27( 21.07%)d 0.00( 0.08%) > 25. (0.00000) RY*( 9) O 2 s( 0.00%)p 1.00( 0.26%)d99.99( 99.74%) > 26. (0.00041) BD*( 1) C 1 - O 2 > ( 71.49%) 0.8455* C 1 s( 24.94%)p 2.99( 74.66%)d 0.02( 0.39%) > 0.0000 0.4639 -0.1850 0.7795 -0.0509 > 0.3691 -0.0133 0.0000 0.0000 0.0347 > 0.0000 0.0000 0.0425 -0.0304 > ( 28.51%) -0.5339* O 2 s( 39.85%)p 1.49( 59.48%)d 0.02( 0.67%) > 0.0000 0.6298 -0.0434 -0.7688 0.0247 > 0.0556 0.0059 0.0000 0.0000 0.0144 > 0.0000 0.0000 0.0697 -0.0403 > 27. (0.00048) BD*( 2) C 1 - O 2 > ( 77.33%) 0.8794* C 1 s( 1.13%)p86.96( 98.32%)d 0.48( 0.55%) > 0.0000 -0.0988 0.0394 -0.3676 0.0137 > 0.9208 -0.0114 0.0000 0.0000 0.0627 > 0.0000 0.0000 -0.0385 0.0065 > ( 22.67%) -0.4761* O 2 s( 1.78%)p54.81( 97.77%)d 0.25( 0.45%) > 0.0000 -0.1332 0.0092 -0.0390 -0.0061 > 0.9880 0.0032 0.0000 0.0000 -0.0656 > 0.0000 0.0000 0.0116 0.0085 > 28. (0.00000) BD*( 3) C 1 - O 2 > ( 77.59%) 0.8809* C 1 s( 0.00%)p 1.00( 99.45%)d 0.01( 0.55%) > ( 22.41%) -0.4734* O 2 s( 0.00%)p 1.00( 99.56%)d 0.00( 0.44%) > > Thank youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> 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> > >