From owner-chemistry@ccl.net Thu Mar 12 01:32:00 2009 From: "Soumya Samineni soumya_samineni-#-rediffmail.com" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38811-090312012243-32253-+oDO7YHSS+xBWwf2EYRiIg!=!server.ccl.net> X-Original-From: "Soumya Samineni" Date: Thu, 12 Mar 2009 01:22:39 -0400 Sent to CCL by: "Soumya Samineni" [soumya_samineni|*|rediffmail.com] Dear all, With the ever increasing computational power, there has been an enormous growth in the theoretical/computational chemistry ( personally i feel the word "Theoretical Chemistry" has been abused by considering it as an alternative word for "Computational chemsitry" by people practising computational chemistry). while people doing computational chemistry are also growing like mushrooms and the volume of pages occupied by it has also exploded, the number of people doing the theoretical chemistry (analytical) is dwindling with time. Any ways: It would be nice to hear comments from the leading (and novice) experts of computational and theoretical chemistry regarding the general feeling of the experimental community (who consider that they toil pretty hard physically for every bit of the sentence they write .. ) that we are "Arm chair scientists", who like to quench our thirst for science sitting before a computer all through the day and gulping loads of liquids !! I hope a small debate would make things more clear. regards Soumya From owner-chemistry@ccl.net Thu Mar 12 02:27:01 2009 From: "Chris Dickson c.n.dickson*sms.ed.ac.uk" To: CCL Subject: CCL:G: IR spectra from Gaussian Message-Id: <-38812-090312003509-26428-TFXcGQDoGHLjx97uZBHcPg]*[server.ccl.net> X-Original-From: Chris Dickson Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Thu, 12 Mar 2009 03:34:55 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Chris Dickson [c.n.dickson]_[sms.ed.ac.uk] Hi all,=0A=0ACan anyone help me find a simple script/program to extract IR = data from a Gaussian03 output file, broaden the peaks, and output a set of = xy data?=0A=0AThanks in advance,=0AChris Dickson=0A From owner-chemistry@ccl.net Thu Mar 12 04:09:00 2009 From: "Daniil Bratashov dn2010(!)gmail.com" To: CCL Subject: CCL:G: IR spectra from Gaussian Message-Id: <-38813-090312040103-7179-p7TKD6LgLjpi3S91RiBNdA ~~ server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 12 Mar 2009 10:11:09 +0300 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010{}gmail.com] On Thu, 12 Mar 2009 03:34:55 +0000 (GMT) "Chris Dickson c.n.dickson*sms.ed.ac.uk" wrote: > Can anyone help me find a simple script/program to extract IR data > from a Gaussian03 output file, broaden the peaks, and output a set of > xy data? gausssum: http://gausssum.sourceforge.net/ windows version has a hidden error in config, simply delete library.zip (or something like .zip file name) from path to gnuplot. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Thu Mar 12 04:44:00 2009 From: "Narendra narendrax^-^gmail.com" To: CCL Subject: CCL:G: IR spectra from Gaussian Message-Id: <-38814-090312043306-18399-vuRGkFisi0kNuf9WBM6Ngg|a|server.ccl.net> X-Original-From: Narendra Content-Type: multipart/alternative; boundary=000e0cd32872521ae30464e7d4b1 Date: Thu, 12 Mar 2009 14:02:49 +0530 MIME-Version: 1.0 Sent to CCL by: Narendra [narendrax|gmail.com] --000e0cd32872521ae30464e7d4b1 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI Chris, The IR data from the output file can be visualized by Gauss View or by a Chemcraft software. On Thu, Mar 12, 2009 at 9:04 AM, Chris Dickson c.n.dickson*sms.ed.ac.uk < owner-chemistry^ccl.net> wrote: > > Sent to CCL by: Chris Dickson [c.n.dickson]_[sms.ed.ac.uk] > > Hi all, > > Can anyone help me find a simple script/program to extract IR data from a > Gaussian03 output file, broaden the peaks, and output a set of xy data? > > Thanks in advance, > Chris Dickson > > > > > - This is automatically added to each message by the mailing script -> > > -- Revanuri S. Narendra Babu, Research Scholar, Goa University. rsnarendra^unigoa.ac.in narendrax^gmail.com --000e0cd32872521ae30464e7d4b1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable HI Chris,
The IR data from the output file can be visualized by Gauss Vi= ew or by a Chemcraft software.

On Thu, M= ar 12, 2009 at 9:04 AM, Chris Dickson c.n.dickson*sms.ed.ac.uk <owner-chemistry^ccl.net> wrote:

Sent to CCL by: Chris Dickson [c.n.dickson]_[sms.ed.ac.uk]

Hi all,

Can anyone help me find a simple script/program to extract IR data from a G= aussian03 output file, broaden the peaks, and output a set of xy data?

Thanks in advance,
Chris Dickson




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Revanuri S. Narendra Ba= bu,
Research Scholar,
Goa University.
rsnarendra^unigoa.ac.in
narendrax^gmail.com
--000e0cd32872521ae30464e7d4b1-- From owner-chemistry@ccl.net Thu Mar 12 05:18:01 2009 From: "Shuwen Yao lilichemistry[a]yahoo.com" To: CCL Subject: CCL: P electrons distribution among the three P orbitals Message-Id: <-38815-090312043822-22409-2RDTRT2msSiDENvGEGjzDA%server.ccl.net> X-Original-From: "Shuwen Yao" Date: Thu, 12 Mar 2009 04:38:19 -0400 Sent to CCL by: "Shuwen Yao" [lilichemistry,+,yahoo.com] Hi, I have a question on my mind these days, which solicits your help. AS we know, and also a result of software calculations, free Carbon atom has two P electrons, which occupy any two of the three P orbitals. On the other hand, As the three P orbitals are degenerate, the two p electrons may evenly distribute among the three P orbitals, resulting in a state with 2/3 electrons on each of the three P orbitals. I am not sure which one is more energically favorable. Hope get your help. Shuwen email: lilichemistry at yaoo.com From owner-chemistry@ccl.net Thu Mar 12 05:54:01 2009 From: "Michel Petitjean petitjean.chiral^_^gmail.com" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38816-090312042504-14981-s0kGHJ+EP7T8BWxHKdgXlQ[]server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 12 Mar 2009 09:24:42 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral%a%gmail.com] Dear All, Here (France), only experimental chemistry is recognized. Tasks requiring computers are often considered as low level secondary tasks, easy to do (or to be done by some student). Proof: the ten years old son of the experimentalist plays on the net all the day, so computer tasks are easy to do (however it may be boring the experimentalist). The true researchers are the experimentalists, and the other ones must serve the experimentalists because they are not true researchers. Only one exception: the quantum chemists (called here "theoretical chemists") constitute a well recognized community, of which many members consider themselves as superior to any other chemist, probably due to the stupid ranking math > physics > chemistry > biology > social sciences and all the rest (quantum chemistry thus appears closer to physics than the rest of chemistry). A consequence is that chem/info people not falling in the quantum chemistry field are ignored, and by no way are considered: difficulties to get funds, evaluation of activity done by quantum chemists who do not care, etc. By the way, please let me know where I can read the definition of the following fields: computational chemistry, theoretical chemistry, mathematical chemistry, quantum chemistry, cheminformatics, chemometrics, structural bioinformatics, molecular modeling. Particularly, I would be interested to know how cheminformatics is defined, and in what it differs from the other fields enumerated above. Finally, in-silico chemists play and do not work. Proof: they have time to read and to write posts in the CCL forum while the experimentalists really work. Thanks. Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean*cea.fr, petitjean.chiral*gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Sent to CCL by: "Soumya Samineni" [soumya_samineni|*|rediffmail.com] Dear all, With the ever increasing computational power, there has been an enormous growth in the theoretical/computational chemistry ( personally i feel the word "Theoretical Chemistry" has been abused by considering it as an alternative word for "Computational chemsitry" by people practising computational chemistry). while people doing computational chemistry are also growing like mushrooms and the volume of pages occupied by it has also exploded, the number of people doing the theoretical chemistry (analytical) is dwindling with time. Any ways: It would be nice to hear comments from the leading (and novice) experts of computational and theoretical chemistry regarding the general feeling of the experimental community (who consider that they toil pretty hard physically for every bit of the sentence they write .. ) that we are "Arm chair scientists", who like to quench our thirst for science sitting before a computer all through the day and gulping loads of liquids !! I hope a small debate would make things more clear. regards Soumya From owner-chemistry@ccl.net Thu Mar 12 06:28:01 2009 From: "=?utf-8?B?bHl6aGFv?= lyzhao _ zjnu.cn" To: CCL Subject: CCL: =?utf-8?B?UmU6IENDTDpHOiBJUiBzcGVjdHJhIGZyb20gR2F1c3NpYW4=?= Message-Id: <-38817-090312053937-19119-oaV2861i2qMW6mcsnstxAg/./server.ccl.net> X-Original-From: "=?utf-8?B?bHl6aGFv?=" Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="utf-8" Date: Thu, 12 Mar 2009 17:06:51 +0800 Mime-Version: 1.0 Sent to CCL by: "=?utf-8?B?bHl6aGFv?=" [lyzhao ~ zjnu.cn] RGVhciBDaHJpcyBEaWNrc29uIGMubi5kaWNrc29uKnNtcy5lZC5hYy51aywNCgkgIHVzZSBHYWJl ZGl0OiBodHRwOi8vZ2FiZWRpdC5zb3VyY2Vmb3JnZS5uZXQvDQoNCkJlc3QgcmVnYXJkcyEhDQog IGx5eg0KICBEYXRlOjIwMDktMDMtMTINCg0KRnJvbe+8mkNocmlzIERpY2tzb24gYy5uLmRpY2tz b24qc21zLmVkLmFjLnVrDQpEYXRl77yaMjAwOS0wMy0xMiAxNDo0NTozNA0KVG/vvJpMYW4sIFlv dXpoYW8gLWlkIzNleC0NCkNj77yaDQpTdWJqZWN077yaQ0NMOkc6IElSIHNwZWN0cmEgZnJvbSBH YXVzc2lhbg0KDQoNClNlbnQgdG8gQ0NMIGJ5OiBDaHJpcyBEaWNrc29uIFtjLm4uZGlja3Nvbl1f W3Ntcy5lZC5hYy51a10NCg0KSGkgYWxsLA0KDQpDYW4gYW55b25lIGhlbHAgbWUgZmluZCBhIHNp bXBsZSBzY3JpcHQvcHJvZ3JhbSB0byBleHRyYWN0IElSIGRhdGEgZnJvbSBhIEdhdXNzaWFuMDMg b3V0cHV0IGZpbGUsIGJyb2FkZW4gdGhlIHBlYWtzLCBhbmQgb3V0cHV0IGEgc2V0IG9mIHh5IGRh dGE/DQoNClRoYW5rcyBpbiBhZHZhbmNlLA0KQ2hyaXMgRGlja3Nvbg0KDQoNCg0KDQotPSBUaGlz IGlzIGF1dG9tYXRpY2FsbHkgYWRkZWQgdG8gZWFjaCBtZXNzYWdlIGJ5IHRoZSBtYWlsaW5nIHNj cmlwdCA9LQ0KVG8gcmVjb3ZlciB0aGUgZW1haWwgYWRkcmVzcyBvZiB0aGUgYXV0aG9yIG9mIHRo ZSBtZXNzYWdlLCBwbGVhc2UgY2hhbmdlDQp0aGUgc3RyYW5nZSBjaGFyYWN0ZXJzIG9uIHRoZSB0 b3AgbGluZSB0byB0aGUgQCBzaWduLiBZb3UgY2FuIGFsc28NCmxvb2sgdXAgdGhlIFgtT3JpZ2lu YWwtRnJvbTogbGluZSBpbiB0aGUgbWFpbCBoZWFkZXIuDQoNCkUtbWFpbCB0byBzdWJzY3JpYmVy czogQ0hFTUlTVFJZQGNjbC5uZXQgb3IgdXNlOg0KICAgICAgaHR0cDovL3d3dy5jY2wubmV0L2Nn aS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UNCg0KRS1tYWlsIHRvIGFkbWluaXN0cmF0b3JzOiBD SEVNSVNUUlktUkVRVUVTVEBjY2wubmV0IG9yIHVzZQ0KICAgICAgaHR0cDovL3d3dy5jY2wubmV0 L2NnaS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UNCg0KU3Vic2NyaWJlL1Vuc3Vic2NyaWJlOiAN CiAgICAgIGh0dHA6Ly93d3cuY2NsLm5ldC9jaGVtaXN0cnkvc3ViX3Vuc3ViLnNodG1sDQoNCkJl Zm9yZSBwb3N0aW5nLCBjaGVjayB3YWl0IHRpbWUgYXQ6IGh0dHA6Ly93d3cuY2NsLm5ldA0KDQpK b2I6IGh0dHA6Ly93d3cuY2NsLm5ldC9qb2JzIA0KQ29uZmVyZW5jZXM6IGh0dHA6Ly9zZXJ2ZXIu Y2NsLm5ldC9jaGVtaXN0cnkvYW5ub3VuY2VtZW50cy9jb25mZXJlbmNlcy8NCg0KU2VhcmNoIE1l c3NhZ2VzOiBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3NlYXJjaGNjbC9pbmRleC5zaHRt bA0KDQpJZiB5b3VyIG1haWwgYm91bmNlcyBmcm9tIENDTCB3aXRoIDUuNy4xIGVycm9yLCBjaGVj azoNCiAgICAgIGh0dHA6Ly93d3cuY2NsLm5ldC9zcGFtbWVycy50eHQNCg0KUlRGSTogaHR0cDov L3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVjdGlvbnMvDQoNCg0K From owner-chemistry@ccl.net Thu Mar 12 09:17:01 2009 From: "lerouvin-.-loria.fr" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38818-090312091340-18419-GoidoYOIwaKigdbs5Ahugw . server.ccl.net> X-Original-From: lerouvin:loria.fr Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 12 Mar 2009 14:13:18 +0100 MIME-Version: 1.0 Sent to CCL by: lerouvin[*]loria.fr Hi Soumya, Well as a {theoretical/computational chemist / molecular modeler / =20 bioinformatician / pick whatever you like} I was sometimes told as =20 being "disconnected from reality" when I tackled some complex tasks =20 involving coding during extended periods of time... Well I probably =20 looked like one of those "armchair scientists" glued to the chair in =20 front of the computer indeed, so no offense... I always took remarks =20 that I was spending too much time "on the dark side" as useful =20 reminders that I should never be careless with validation. Colleagues more versed on the experimental side of chemistry might as =20 well try to perform synthesis projects so time-consuming, complex and =20 exotic that they end up looking like "mad professors" - the movie type =20 always ready to attempt ramdom and often disastrous experiments in a =20 creepy basement. If you spot one that dared to call you an "armchair =20 scientist" in the past, then it's payback time ;-) VL "Soumya Samineni soumya_samineni-#-rediffmail.com" =20 a =E9crit=A0: > > Sent to CCL by: "Soumya Samineni" [soumya_samineni|*|rediffmail.com] > Dear all, > With the ever increasing computational power, there has been an =20 > enormous growth in the theoretical/computational chemistry ( =20 > personally i feel the word "Theoretical Chemistry" has been abused =20 > by considering it as an alternative word for "Computational =20 > chemsitry" by people practising computational chemistry). while =20 > people doing computational chemistry are also growing like mushrooms =20 > and the volume of pages occupied by it has also exploded, the =20 > number of people doing the theoretical chemistry (analytical) is =20 > dwindling with time. > Any ways: It would be nice to hear comments from the leading (and =20 > novice) experts of computational and theoretical chemistry regarding =20 > the general feeling of the experimental community (who consider =20 > that they toil pretty hard physically for every bit of the sentence =20 > they write .. ) that we are "Arm chair scientists", who like to =20 > quench our thirst for science sitting before a computer all through =20 > the day and gulping loads of liquids !! > > I hope a small debate would make things more clear. > > regards > Soumya > > From owner-chemistry@ccl.net Thu Mar 12 09:52:00 2009 From: "Volker Haehnke haehnke..:..bioinformatik.uni-frankfurt.de" To: CCL Subject: CCL: Simulating 1H NMR Spectra Message-Id: <-38819-090312070228-30674-YRhPAYxm/xGGuQh9ZPYsiQ.:.server.ccl.net> X-Original-From: "Volker Haehnke" Date: Thu, 12 Mar 2009 07:02:24 -0400 Sent to CCL by: "Volker Haehnke" [haehnke()bioinformatik.uni-frankfurt.de] Dear fellow members of the CCL mailinglist, at the moment I have a little problem I'm not so sure how to solve, and I hope someone on this list can help me: I need to know the the value of an part of the integral in the 1H spectra of many compounds (available as SDF files), for example the integral between 1 and 2 ppm in the spectrum of chlorpromazine. As I can not expect that the spectrum of every compound is available somewhere, I think it is safe to assume that I need at first a way to simulate the complete spectrum. What I tried so far was to use tools like ChemOffice to simulate the spectrum. The idea was to save it as some kind of image and then compute (or simply count) the integral values I need below the painted line. But that does not work as I wished. Because the simulated peaks are so narrow, they consist only out of the painted lines, so there is no area I could try to estimate. And none of the tools I found so far offers some kind of batch mode, so I would have to process every molecule by hand. To try to implement my own spectra simulation seems not so promising, besides that so far I couldn't find much on that topic. So my question: does anyone know a (preferred simple) solution for my problem - to get the integral values in a certain interval of the 1H spectra of compounds that are available as SDF files? Kind regards Volker Haehnke haehnke~~bioinformatik.uni-frankfurt.de From owner-chemistry@ccl.net Thu Mar 12 10:32:00 2009 From: "Serdar Badoglu sbadoglu:-:gazi.edu.tr" To: CCL Subject: CCL:G: IR spectra from Gaussian Message-Id: <-38820-090312034332-5769-rjXHXTnS9TaOrdjJSlrc0g,server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Thu, 12 Mar 2009 03:43:28 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu,,gazi.edu.tr] Dear Chris, I don't know if any such script/program exists. But here's an alternative way I follow: Right click on the Gaussian03's IR spectrum graph and select "save data". There you can also determine the initial and final wavenumbers which you're interested in, and the stepsize as well. Extracted data will be saved as a text file, later you can import those data to SigmaPlot or a similar spreadsheet software (I always recommend to use scientific spreadsheet programs). Hope this helps, Serdar Badoglu From owner-chemistry@ccl.net Thu Mar 12 11:02:01 2009 From: "Roman D Gorbunov rgorbuno{}aecom.yu.edu" To: CCL Subject: CCL:G: Error imposing constraints in Gaussian Message-Id: <-38821-090312103720-2183-eDAy5arUVRUdMo0s1jdFiw ~ server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Thu, 12 Mar 2009 10:37:15 -0400 Sent to CCL by: "Roman D Gorbunov" [rgorbuno-,-aecom.yu.edu] Dear CCL Subscribers, I try to run a geometry optimization in which the structure of the molecule is restricted to be planar (this is a 2 nucleotide system, a base-pare). My calculation crashed. In the end I have the following message: Iteration100 RMS(Cart)= 0.00004173 RMS(Int)= 0.00140344 New curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in /opt/g03/l103.exe at Mon Mar 9 13:29:22 2009. Job cpu time: 0 days 6 hours 9 minutes 54.8 seconds. File lengths (MBytes): RWF= 134 Int= 0 D2E= 0 Chk= 20 Scr= 1 I found that in the CCL list peoples already discussed this problem: http://server.ccl.net/cgi-bin/ccl/message-new?2003+05+23+007. However, this message does not help me. It is written there that the problem can appear if "the fixed torsional or dihedral angles are far from that of the starting geometry". It is not my case since I do NOT have 2 values for the same coordinate("starting" one and "fixed" one). For every internal coordinate I have only one value and than in the end of the input file I specify the internal coordinates which have to be fixed. In the cited message also written that problem can appear if "you fix too many redundant coordinates at once causing Gaussian to have a difficult time funneling the forces in the remaining coordinates". It seams to be my case. I fix a lot of dihedral angles to force the structure to be planar. So, i probably know what is the reason of the problem but I still do not know how to solve the problem. Can anybody help me with that? Thank you in advance, Roman. From owner-chemistry@ccl.net Thu Mar 12 11:37:01 2009 From: "Yutao Yue Yutao.Yue#,#gmail.com" To: CCL Subject: CCL:G: (correction) Energy change upon swapping two orbitals in Gaussian 98 Message-Id: <-38822-090312105457-17527-GNMRUcyRUaIRAk0WnAy9kw-$-server.ccl.net> X-Original-From: "Yutao Yue" Date: Thu, 12 Mar 2009 10:54:53 -0400 Sent to CCL by: "Yutao Yue" [Yutao.Yue- -gmail.com] (sorry the energy changes are 0.02 a.u., NOT 0.2 a.u.) Dear All, I have a successful G98 single point calculation (UBLYP/6-31G*) on a metal-containing system of around 70 atoms. I use the result MOs as initial guess, but swapped the two highest occupied beta orbitals (which are supposed to be highly competing with each other) upon reading in the initial guess, to do another G98 single point calculation on the same system. I then arrived at a solution that, the frontier orbitals are almost identical to the original solution including the ordering of the beta orbitals, while the single point energy is 0.02 a.u. lower! Similar calculations was done with UBPW91/6-31G*, and again the orbitals go back to original ordering, but the single point energy is 0.02 a.u. higher now! Anybody have any idea about those energy changes? Thanks a lot and wish everybody a nice day! -Yutao Yue From owner-chemistry@ccl.net Thu Mar 12 12:21:01 2009 From: "Richard Tia richtiagh*|*gmail.com" To: CCL Subject: CCL: Pi complex vrs reactants Message-Id: <-38823-090312121740-31513-oB4mxsLHohZUVKDDCjYRGw##server.ccl.net> X-Original-From: "Richard Tia" Date: Thu, 12 Mar 2009 12:17:36 -0400 Sent to CCL by: "Richard Tia" [richtiagh(_)gmail.com] Hi Everybody, Is it reasonable for a pi-complex to be higher in energy than the reactants from which it is formed? What will be the likely reason for such an occurrence? Or am I doing something wrong in my calculations( DFT B3LYP/6-31G*)? I'll be glad if someone can offer me some insight. Thanks in advance for your help. Best regards. Richard Tia Department of Chemistry KNUST Kumasi, GHANA From owner-chemistry@ccl.net Thu Mar 12 12:55:01 2009 From: "Johannes Hachmann jh388~!~cornell.edu" To: CCL Subject: CCL:G: (correction) Energy change upon swapping two orbitals in Gaussian 98 Message-Id: <-38824-090312125119-19908-ukTunfjnm+qrDsvLwUZNXA:-:server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 12 Mar 2009 12:50:56 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh388]*[cornell.edu] Dear Yutao, sounds to me like you might have landed on an electronic instability the first time. SCF for (transition-)metal compounds can be very hard to converge. Try STABLE=OPT starting from your original calc without the orbital swap and see whether that lowers the energy (in that case, your swap has introduced some mixing/symmetry breaking and led to a more stable state). You can check the S2 value of your two results to see, whether your state has changed. You might also want to check your SCF convergence threshold and DFT grid (although it should not make a difference of 20mH). Generally, swapping the highest two HOMOs should not change the energy at all, but maybe you ment the HOMO-LUMO pair? A vanishing HOMO-LUMO gap indicates a system with nondynamic correlation, and you might not want to use a single reference method like DFT in the first place. Hope that helps. Best Johannes --------------------------------------------------------------- Johannes Hachmann Chan Research Group 140D Baker Laboratory Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853-1301 USA --------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh388==cornell.edu_-_ccl.net > [mailto:owner-chemistry+jh388==cornell.edu_-_ccl.net] On Behalf > Of Yutao Yue Yutao.Yue#,#gmail.com > Sent: Thursday, March 12, 2009 10:55 AM > To: Hachmann, Johannes > Subject: CCL:G: (correction) Energy change upon swapping two > orbitals in Gaussian 98 > > > Sent to CCL by: "Yutao Yue" [Yutao.Yue- -gmail.com] (sorry > the energy changes are 0.02 a.u., NOT 0.2 a.u.) > > Dear All, > > I have a successful G98 single point calculation > (UBLYP/6-31G*) on a metal-containing system of around 70 > atoms. I use the result MOs as initial guess, but swapped the > two highest occupied beta orbitals (which are supposed to be > highly competing with each other) upon reading in the initial > guess, to do another G98 single point calculation on the same > system. I then arrived at a solution that, the frontier > orbitals are almost identical to the original solution > including the ordering of the beta orbitals, while the single > point energy is 0.02 a.u. lower! > > Similar calculations was done with UBPW91/6-31G*, and again > the orbitals go back to original ordering, but the single > point energy is 0.02 a.u. higher now! > > Anybody have any idea about those energy changes? > > Thanks a lot and wish everybody a nice day! > > -Yutao Yue > > > > -= 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 look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Thu Mar 12 13:30:00 2009 From: "Rene Fournier renef..yorku.ca" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38825-090312123316-12008-XSdmh3DlMr8UpzK6pPCMzA-#-server.ccl.net> X-Original-From: Rene Fournier Content-Transfer-Encoding: 8BIT Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Date: Thu, 12 Mar 2009 10:55:04 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Rene Fournier [renef##yorku.ca] Hello Soumya, >the general feeling of the experimental community (who consider that >they toil pretty hard physically for every bit of the sentence they >write .. ) that we are "Arm chair scientists", For the record: I'm a computational chemist, I think... Generally, I find that my experimental colleagues have a much better understanding, and appreciation, of comp/theo chemistry now than they had 20 years ago, when I started. Many of them have someone in their group who does calculations. They get a lot out of those calculations, but at the same time they realize that there are pitfalls, that you need expertise and careful analysis to get something meaningful out of even the most black-box of programs. I think many of them now view computers and software (comp chem packages) similarly to how they view X-ray diffraction, or NMR: a powerful tool, that's reached a certain maturity, so that it's easy enough to use and accurate enough to be useful to non-specialists. I suppose they view "computational chemists" the same way they view experimentalists who specialize in developing new methods in NMR/synchrotron radiation/lasers/... or are expert in using the most advanced of those techniques. They probably view people who do only routine computations the same way they view people who do only routine X-ray structures --- a technician's work, not a basis for an original research program. At my university, many experimentalists spend a lot of time in front of their computer! They look at spectra, data, fits, graphics, etc. generated by instruments operated by their students and PDF, and they try to make sense of it all. It's not SO different from a computational chemist spending time in front of the computer looking at data, fits, graphics, etc. generated by a software "operated" by themselves or students. A bigger difference, maybe, is in how each one tries to make sense of the data, whether it was generated in labo, or in silico. I find that "experimentalists" often have a very sophisticated understanding of theory, more so than many "computationalists". In our chemistry department of ~30 faculty members there is: an organic chemist who "turned computational" >20 years ago and now does exclusively computations; a theoretical/computational chemist who turned "experimental" but kept doing calculations and then returned to (mostly) theory and computation; an emeritus professor who was among the first to do MO calculations in the 1950's, then did exclusively experiments for the following 40 years (not having access to a computer it rather difficult to do MO calculations...) and then went back to MO and MD near his retirement age; and at least 3 faculty members who are primarily experimentalists but for whom computations play an essential part. One thing I hear experimentalists sometimes say is that we have it easy compared to them with "bugs": it's usually a lot tougher to set up a new experiment or new instrument than writing a new piece of code! That's probably true. But then, when they use computation/theory, they normally don't write their own code, so they see only the easiest aspect of computing. -- Rene Rene Fournier Office: 303 Petrie Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 4700 Keele Street, Toronto FAX: (416)-736-5936 Ontario, CANADA M3J 1P3 e-mail: renef+*+yorku.ca On Thu, 12 Mar 2009, lerouvin-.-loria.fr wrote: > > Sent to CCL by: lerouvin[*]loria.fr > > Hi Soumya, > > Well as a {theoretical/computational chemist / molecular modeler / > bioinformatician / pick whatever you like} I was sometimes told as > being "disconnected from reality" when I tackled some complex tasks > involving coding during extended periods of time... Well I probably > looked like one of those "armchair scientists" glued to the chair in > front of the computer indeed, so no offense... I always took remarks > that I was spending too much time "on the dark side" as useful > reminders that I should never be careless with validation. > > Colleagues more versed on the experimental side of chemistry might as > well try to perform synthesis projects so time-consuming, complex and > exotic that they end up looking like "mad professors" - the movie type > always ready to attempt ramdom and often disastrous experiments in a > creepy basement. If you spot one that dared to call you an "armchair > scientist" in the past, then it's payback time ;-) > > VL > > > "Soumya Samineni soumya_samineni-#-rediffmail.com" > a écrit : > > > > > Sent to CCL by: "Soumya Samineni" [soumya_samineni|*|rediffmail.com] > > Dear all, > > With the ever increasing computational power, there has been an > > enormous growth in the theoretical/computational chemistry ( > > personally i feel the word "Theoretical Chemistry" has been abused > > by considering it as an alternative word for "Computational > > chemsitry" by people practising computational chemistry). while > > people doing computational chemistry are also growing like mushrooms > > and the volume of pages occupied by it has also exploded, the > > number of people doing the theoretical chemistry (analytical) is > > dwindling with time. > > Any ways: It would be nice to hear comments from the leading (and > > novice) experts of computational and theoretical chemistry regarding > > the general feeling of the experimental community (who consider > > that they toil pretty hard physically for every bit of the sentence > > they write .. ) that we are "Arm chair scientists", who like to > > quench our thirst for science sitting before a computer all through > > the day and gulping loads of liquids !! > > > > I hope a small debate would make things more clear. > > > > regards > > Soumya > > > > > > > > -> > > > From owner-chemistry@ccl.net Thu Mar 12 14:53:01 2009 From: "Patricia Richardson Patricia.Richardson^-^ed.ac.uk" To: CCL Subject: CCL:G: IR spectra from Gaussian Message-Id: <-38826-090312100729-14247-P4RThcxMw2gmP3S6rwjwkA#,#server.ccl.net> X-Original-From: Patricia Richardson Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 12 Mar 2009 13:31:12 +0000 MIME-Version: 1.0 Sent to CCL by: Patricia Richardson [Patricia.Richardson(-)ed.ac.uk] Hello, Gabedit is quite good. You can also use it to visualise the vibrational mode= s. Best wishes, Tricia Quoting "Daniil Bratashov dn2010(!)gmail.com" : > > Sent to CCL by: Daniil Bratashov [dn2010{}gmail.com] > On Thu, 12 Mar 2009 03:34:55 +0000 (GMT) > "Chris Dickson c.n.dickson*sms.ed.ac.uk" > wrote: > >> Can anyone help me find a simple script/program to extract IR data >> from a Gaussian03 output file, broaden the peaks, and output a set of >> xy data? > > gausssum: http://gausssum.sourceforge.net/ > > windows version has a hidden error in config, simply delete library.zip > (or something like .zip file name) from path to gnuplot. > > WBR, Daniil Bratashov. > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > > ****************************************************************************= **** EaStCHEM Research Computing Officer School of Chemistry Tel: 0131 650 7748 University of Edinburgh Fax: 0131 650 6453 West Mains Road Edinburgh EH9 3JJ ****************************************************************************= **** --=20 The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From owner-chemistry@ccl.net Thu Mar 12 16:23:01 2009 From: "Tanja van Mourik tanja.vanmourik()st-andrews.ac.uk" To: CCL Subject: CCL: Pi complex vrs reactants Message-Id: <-38827-090312160356-18596-eNfTnMjv7ml13FVR/qESnA*server.ccl.net> X-Original-From: Tanja van Mourik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 12 Mar 2009 19:32:58 +0000 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik .. st-andrews.ac.uk] Hi Richard, > Is it reasonable for a pi-complex to be higher in energy than the reactants from which it is formed? What will be the likely reason for such an occurrence? > Or am I doing something wrong in my calculations( DFT B3LYP/6-31G*)? > I'll be glad if someone can offer me some insight. B3LYP does not describe dispersion, and therefore underestimates the interaction energies of pi-bonded systems. This may well result in a repulsive interaction. See for example: A critical note on density functional theory for studies on rare-gas dimers, J. Chem. Phys. 116, 9620 (2002) Chem. Phys. 304, 317 (2004) (on indole-water) Assessment of density functional for intramolecular disperison-rich interactions, J. Chem. Theor. Comp. 4, 1610 (2009) You may want to consider density functionals that are better for dispersion interactions, such as the Truhlar functionals (M05-2X, M06-2X, ...), double hybrid functionals (like B2-PLYP) or DFT-D (DFT augmented with an empirical dispersion term). If you can afford ab initio methods, SCS-MP2 may be a good option (as regular MP2 tends to overestimate dispersion interactions). Hope this helps, Tanja -- ================================================================ Tanja van Mourik Senior Lecturer in Chemistry School of Chemistry, University of St. Andrews North Haugh, St. Andrews, Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik() st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm The University of St Andrews is a charity registered in Scotland: No SC013532 ================================================================ From owner-chemistry@ccl.net Thu Mar 12 16:57:00 2009 From: "Jim Kress ccl_nospam * kressworks.com" To: CCL Subject: CCL: Computational Chemistry - Arm chair Scientists !!! Message-Id: <-38828-090312161841-19973-2JX7+F8Y15TXmMuPf+bhSg(-)server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 12 Mar 2009 15:07:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam[-]kressworks.com] Personally, I don't have the time or the necessity for all this ego inflation. I am a chemist who will use whatever tools are available to answers the questions that interest me. If that offends someone else or causes them = to think less of me, that's their problem. I don't give a damn what other people think about me or my work or how I get it done. Jim=20 > -----Original Message----- > From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com.:.ccl.net=20 > [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com.:.ccl.net]=20 > On Behalf Of Rene Fournier renef..yorku.ca > Sent: Thursday, March 12, 2009 11:55 AM > To: Kress, Jim > Subject: CCL: Computational Chemistry - Arm chair Scientists !!! >=20 >=20 > Sent to CCL by: Rene Fournier [renef##yorku.ca] Hello Soumya, >=20 > >the general feeling of the experimental community (who consider that=20 > >they toil pretty hard physically for every bit of the sentence they=20 > >write .. ) that we are "Arm chair scientists", >=20 > For the record: I'm a computational chemist, I think... =20 > Generally, I find that my experimental colleagues have a much=20 > better understanding, and appreciation, of comp/theo=20 > chemistry now than they had 20 years ago, when I started. =20 > Many of them have someone in their group who does=20 > calculations. They get a lot out of those calculations, but=20 > at the same time they realize that there are pitfalls, that=20 > you need expertise and careful analysis to get something=20 > meaningful out of even the most black-box of programs. I=20 > think many of them now view computers and software (comp chem=20 > packages) similarly to how they view X-ray diffraction, or=20 > NMR: a powerful tool, that's reached a certain maturity, so=20 > that it's easy enough to use and accurate enough to be useful=20 > to non-specialists. > I suppose they view "computational chemists" the same way=20 > they view experimentalists who specialize in developing new=20 > methods in NMR/synchrotron radiation/lasers/... or are=20 > expert in using the most advanced of those techniques. > They probably view people who do only routine computations=20 > the same way they view people who do only routine X-ray=20 > structures --- a technician's work, not a basis for an=20 > original research program. > At my university, many experimentalists spend a lot of=20 > time in front of their computer! They look at spectra, data,=20 > fits, graphics, etc. generated by instruments operated by=20 > their students and PDF, and they try to make sense of it all.=20 > It's not SO different from a computational chemist spending=20 > time in front of the computer looking at data, fits,=20 > graphics, etc. generated by a software "operated" by=20 > themselves or students. A bigger difference, maybe, is in=20 > how each one tries to make sense of the data, whether it was=20 > generated in labo, or in silico. I find that=20 > "experimentalists" often have a very sophisticated=20 > understanding of theory, more so than many "computationalists". > In our chemistry department of ~30 faculty members there=20 > is: an organic chemist who "turned computational" >20 years=20 > ago and now does exclusively computations; a=20 > theoretical/computational chemist who turned "experimental" > but kept doing calculations and then returned to (mostly)=20 > theory and computation; an emeritus professor who was among=20 > the first to do MO calculations in the 1950's, then did=20 > exclusively experiments for the following 40 years (not=20 > having access to a computer it rather difficult to do MO=20 > calculations...) and then went back to MO and MD near his=20 > retirement age; and at least 3 faculty members who are=20 > primarily experimentalists but for whom computations play an=20 > essential part. > One thing I hear experimentalists sometimes say is that we=20 > have it easy compared to them with "bugs": it's usually a lot=20 > tougher to set up a new experiment or new instrument than=20 > writing a new piece of code! > That's probably true. But then, when they use=20 > computation/theory, they normally don't write their own code,=20 > so they see only the easiest aspect of computing. >=20 > -- Rene > =20 > Rene Fournier Office: 303 Petrie > Chemistry Dpt, York University Phone: (416) 736 2100 Ext. 30687 > 4700 Keele Street, Toronto FAX: (416)-736-5936 > Ontario, CANADA M3J 1P3 e-mail: renef(~)yorku.ca >=20 >=20 > On Thu, 12 Mar 2009, lerouvin-.-loria.fr wrote: >=20 > >=20 > > Sent to CCL by: lerouvin[*]loria.fr > >=20 > > Hi Soumya, > >=20 > > Well as a {theoretical/computational chemist / molecular modeler /=20 > > bioinformatician / pick whatever you like} I was sometimes told as=20 > > being "disconnected from reality" when I tackled some complex tasks=20 > > involving coding during extended periods of time... Well I probably=20 > > looked like one of those "armchair scientists" glued to the=20 > chair in=20 > > front of the computer indeed, so no offense... I always=20 > took remarks=20 > > that I was spending too much time "on the dark side" as useful=20 > > reminders that I should never be careless with validation. > >=20 > > Colleagues more versed on the experimental side of=20 > chemistry might as=20 > > well try to perform synthesis projects so time-consuming,=20 > complex and=20 > > exotic that they end up looking like "mad professors" - the=20 > movie type=20 > > always ready to attempt ramdom and often disastrous=20 > experiments in a=20 > > creepy basement. If you spot one that dared to call you an=20 > "armchair=20 > > scientist" in the past, then it's payback time ;-) > >=20 > > VL > >=20 > >=20 > > "Soumya Samineni soumya_samineni-#-rediffmail.com" =20 > > a =E9crit=A0: > >=20 > > > > > > Sent to CCL by: "Soumya Samineni"=20 > [soumya_samineni|*|rediffmail.com] > > > Dear all, > > > With the ever increasing computational power, there=20 > has been an =20 > > > enormous growth in the theoretical/computational chemistry ( =20 > > > personally i feel the word "Theoretical Chemistry" has=20 > been abused =20 > > > by considering it as an alternative word for "Computational =20 > > > chemsitry" by people practising computational chemistry). while =20 > > > people doing computational chemistry are also growing=20 > like mushrooms =20 > > > and the volume of pages occupied by it has also exploded, the =20 > > > number of people doing the theoretical chemistry=20 > (analytical) is =20 > > > dwindling with time. > > > Any ways: It would be nice to hear comments from the=20 > leading (and =20 > > > novice) experts of computational and theoretical=20 > chemistry regarding =20 > > > the general feeling of the experimental community (who consider =20 > > > that they toil pretty hard physically for every bit of=20 > the sentence =20 > > > they write .. ) that we are "Arm chair scientists", who like to =20 > > > quench our thirst for science sitting before a computer=20 > all through =20 > > > the day and gulping loads of liquids !! > > > > > > I hope a small debate would make things more clear. > > > > > > regards > > > Soumya > > > > > > > >=20 > >=20 > >=20 > > ->=20 > >=20 > >=20 > > >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing=20 > script =3D- > To recover the email address of the author of the message,=20 > please change>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 From owner-chemistry@ccl.net Thu Mar 12 17:35:01 2009 From: "Yutao Yue yutao.yue:-:gmail.com" To: CCL Subject: CCL:G: (correction) Energy change upon swapping two orbitals in Gaussian 98 Message-Id: <-38829-090312152241-7246-NCpakEih7xyYisKSS1CO+Q-,-server.ccl.net> X-Original-From: Yutao Yue Content-Type: multipart/alternative; boundary=0016e647622480c46e0464f0d059 Date: Thu, 12 Mar 2009 15:15:59 -0400 MIME-Version: 1.0 Sent to CCL by: Yutao Yue [yutao.yue|a|gmail.com] --0016e647622480c46e0464f0d059 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Thank you very much Johannes, I did swap the two highest OCCUPIED beta orbitals. I was also doubting that the original solution was not stable. I compared the solutions before and after swapping, the MO compositions are almost identical for frontier orbitals, and only some minor differences for some deeper orbitals. Plus, the S2 values, the NBO charges and spins of some characteristic atoms (metal, etc) are almost exactly the same, up to quite a few digits. On the other hand, although with highly similar MO compositions, the MO energy themselves are fairly different through all MOs including the deepest, e.g., the difference for a single MO is on the order of 0.01 a.u.. By the way, I used the default SCF convergence level (which is equivalent to conver=4). But I guess that's far from introducing errors of this magnitude right? I wonder is it possible that Gaussian does something artificial (and arbitrary? because in one case energy went up and the other case it went down) to the MO energies, once the initial guess swapping is introduced? Regards, Yutao On Thu, Mar 12, 2009 at 12:50 PM, Johannes Hachmann jh388~!~cornell.edu < owner-chemistry%ccl.net> wrote: > > Sent to CCL by: "Johannes Hachmann" [jh388]*[cornell.edu] > Dear Yutao, > > sounds to me like you might have landed on an electronic instability the > first time. SCF for (transition-)metal compounds can be very hard to > converge. Try STABLE=OPT starting from your original calc without the > orbital swap and see whether that lowers the energy (in that case, your > swap > has introduced some mixing/symmetry breaking and led to a more stable > state). You can check the S2 value of your two results to see, whether your > state has changed. You might also want to check your SCF convergence > threshold and DFT grid (although it should not make a difference of 20mH). > > Generally, swapping the highest two HOMOs should not change the energy at > all, but maybe you ment the HOMO-LUMO pair? A vanishing HOMO-LUMO gap > indicates a system with nondynamic correlation, and you might not want to > use a single reference method like DFT in the first place. > > Hope that helps. Best > > Johannes > > --------------------------------------------------------------- > Johannes Hachmann > > Chan Research Group > 140D Baker Laboratory > Department of Chemistry and Chemical Biology > Cornell University > Ithaca, NY 14853-1301 > USA > --------------------------------------------------------------- > > > > > -----Original Message----- > > From: owner-chemistry+jh388==cornell.edu-.-ccl.net > > [mailto:owner-chemistry+jh388 ==cornell.edu-.- > ccl.net] On Behalf > > Of Yutao Yue Yutao.Yue#,#gmail.com > > Sent: Thursday, March 12, 2009 10:55 AM > > To: Hachmann, Johannes > > Subject: CCL:G: (correction) Energy change upon swapping two > > orbitals in Gaussian 98 > > > > > > Sent to CCL by: "Yutao Yue" [Yutao.Yue- -gmail.com] (sorry > > the energy changes are 0.02 a.u., NOT 0.2 a.u.) > > > > Dear All, > > > > I have a successful G98 single point calculation > > (UBLYP/6-31G*) on a metal-containing system of around 70 > > atoms. I use the result MOs as initial guess, but swapped the > > two highest occupied beta orbitals (which are supposed to be > > highly competing with each other) upon reading in the initial > > guess, to do another G98 single point calculation on the same > > system. I then arrived at a solution that, the frontier > > orbitals are almost identical to the original solution > > including the ordering of the beta orbitals, while the single > > point energy is 0.02 a.u. lower! > > > > Similar calculations was done with UBPW91/6-31G*, and again > > the orbitals go back to original ordering, but the single > > point energy is 0.02 a.u. higher now! > > > > Anybody have any idea about those energy changes? > > > > Thanks a lot and wish everybody a nice day! > > > > -Yutao Yue > > > > > > > > -= 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 look up the X-Original-From: line > > in the mail header.> Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > --0016e647622480c46e0464f0d059 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thank you very much Johannes, I did swap the two highest OCCUPIED beta orbi= tals. I was also doubting that the original solution was not stable. I comp= ared the solutions before and after swapping, the MO compositions are almos= t identical for frontier orbitals, and only some minor differences for some= deeper orbitals. Plus, the S2 values, the NBO charges and spins of some ch= aracteristic atoms (metal, etc) are almost exactly the same, up to quite a = few digits.

On the other hand, although with highly similar MO compositions, the MO= energy themselves are fairly different through all MOs including the deepe= st, e.g., the difference for a single MO is on the order of 0.01 a.u..

By the way, I used the default SCF convergence level (which is equivale= nt to conver=3D4). But I guess that's far from introducing errors of th= is magnitude right?

I wonder is it possible that Gaussian does somet= hing artificial (and arbitrary? because in one case energy went up and the = other case it went down) to the MO energies, once the initial guess swappin= g is introduced?

Regards,
Yutao

On Thu, Mar 12, 200= 9 at 12:50 PM, Johannes Hachmann jh388~!~cor= nell.edu <owner-chemistry%ccl.net> wrote:

Sent to CCL by: "Johannes Hachmann" [jh388]*[cornell.edu]
Dear Yutao,

sounds to me like you might have landed on an electronic instability the first time. SCF for (transition-)metal compounds can be very hard to
converge. Try STABLE=3DOPT starting from your original calc without the
orbital swap and see whether that lowers the energy (in that case, your swa= p
has introduced some mixing/symmetry breaking and led to a more stable
state). You can check the S2 value of your two results to see, whether your=
state has changed. You might also want to check your SCF convergence
threshold and DFT grid (although it should not make a difference of 20mH).<= br>
Generally, swapping the highest two HOMOs should not change the energy at all, but maybe you ment the HOMO-LUMO pair? A vanishing HOMO-LUMO gap
indicates a system with nondynamic correlation, and you might not want to use a single reference method like DFT in the first place.

Hope that helps. Best

Johannes

---------------------------------------------------------------
Johannes Hachmann

Chan Research Group
140D Baker Laboratory
Department of Chemistry and Chemical Biology
Cornell University
Ithaca, NY 14853-1301
USA
---------------------------------------------------------------



> -----Original Message-----
> From: owner-chemistry+jh388=3D=3Dcornell.edu-.-ccl.net
> [mailto:owner-chemistry+jh3= 88=3D=3Dcornell.edu-.-ccl.= net] On Behalf
> Of Yutao Yue Yutao.Yue#,#gmail.com
> Sent: Thursday, March 12, 2009 10:55 AM
> To: Hachmann, Johannes
> Subject: CCL:G: (correction) Energy change upon swapping two
> orbitals in Gaussian 98
>
>
> Sent to CCL by: "Yutao =A0Yue" [Yutao.Yue- -gmail.com] (sorry
> the energy changes are 0.02 a.u., NOT 0.2 a.u.)
>
> Dear All,
>
> I have a successful G98 single point calculation
> (UBLYP/6-31G*) on a metal-containing system of around 70
> atoms. I use the result MOs as initial guess, but swapped the
> two highest occupied beta orbitals (which are supposed to be
> highly competing with each other) upon reading in the initial
> guess, to do another G98 single point calculation on the same
> system. I then arrived at a solution that, the frontier
> orbitals are almost identical to the original solution
> including the ordering of the beta orbitals, while the single
> point energy is 0.02 a.u. lower!
>
> Similar calculations was done with UBPW91/6-31G*, and again
> the orbitals go back to original ordering, but the single
> point energy is 0.02 a.u. higher now!
>
> Anybody have any idea about those energy changes?
>
> Thanks a lot and wish everybody a nice day!
>
> -Yutao Yue
>
>
>
> -=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.> Conferences:

--0016e647622480c46e0464f0d059--