From owner-chemistry@ccl.net Tue Sep 3 02:31:00 2013 From: "Marcel Swart marcel.swart-*-icrea.cat" To: CCL Subject: CCL:G: Dipole Moment Calculation within Gaussian Message-Id: <-49131-130903022910-12033-bvUGZXQ54wNX6W7bCBH09w^_^server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary="Apple-Mail=_98496ACC-D22B-4A7A-B674-85EE13318A5D" Date: Tue, 3 Sep 2013 08:28:59 +0200 Mime-Version: 1.0 (Mac OS X Mail 6.5 \(1508\)) Sent to CCL by: Marcel Swart [marcel.swart()icrea.cat] --Apple-Mail=_98496ACC-D22B-4A7A-B674-85EE13318A5D Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 It should be added that the dipole moment DOES change for charged = species, but maybe this was already mentioned before. On 03 Sep 2013, at 02:28, "Salter-Duke, Brian James = brian.james.duke[]gmail.com" wrote: >> Are the cartesian components of the dipole moment shown in the = gaussian >> output based on a center of mass, center of charge, or geometric = center for >> the origin? If the last, is that based on the "Input Orientation" or = the >> "Standard Orientation"? >>=20 >> I did not find this info when I dove Gaussian's web pages nor a = simple >> google search. Any help would be greatly appreciated. >=20 > I got an answer to this exact question from Gaussian only last week. = The > dipole integrals are evaluated with whatever origin Gaussian is using > for the coordinates . These are normally the "Standard Orientation" > coordinates and these are based on the origin at the centre of charge. > There is an IOP code to use the centre of mass. >=20 > As another poster has said, this does not affect the dipole moment, = but > it defines the x, y, z axis for the cartesian components. >=20 > Brian. =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional i Cat=E0lisi Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart]_[icrea.cat marcel.swart]_[udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail=_98496ACC-D22B-4A7A-B674-85EE13318A5D Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 It = should be added that the dipole moment DOES change for charged = species,
but maybe this was already mentioned = before.

On 03 Sep 2013, at 02:28, "Salter-Duke, = Brian James brian.james.duke[]gmail.com" <owner-chemistry]_[ccl.net> = wrote:

Are = the cartesian components of the dipole moment shown in the = gaussian
output based on a center of mass, center of charge, or = geometric center for
the origin?  If the last, is that based on = the "Input Orientation" or the
"Standard Orientation"?

I did = not find this info when I dove Gaussian's web pages nor a = simple
google search.  Any help would be greatly = appreciated.

I got an answer to this exact = question from Gaussian only last week. The
dipole integrals are = evaluated with whatever origin Gaussian is using

coordinates and these are based on the = origin at the centre of charge.
There is an IOP code to use = the centre of mass.

it defines the x, y, z axis for the = cartesian components.



=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
dr. = Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica = Computacional i Cat=E0lisi
Universitat de Girona

Facultat de = Ci=E8ncies
Campus Montilivi
17071 Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart]_[icrea.cat
marce= l.swart]_[udg.edu
web
http://www.marcelswart.eu
vCard


= --Apple-Mail=_98496ACC-D22B-4A7A-B674-85EE13318A5D-- From owner-chemistry@ccl.net Tue Sep 3 03:37:00 2013 From: "Kurt De Grave Kurt.DeGrave%x%cs.kuleuven.be" To: CCL Subject: CCL: QSPR data mining Message-Id: <-49132-130903033402-6695-xRYlwkS/+Mw7a5roXlYdhA/a\server.ccl.net> X-Original-From: Kurt De Grave Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 03 Sep 2013 09:33:38 +0200 MIME-Version: 1.0 Sent to CCL by: Kurt De Grave [Kurt.DeGrave|*|cs.kuleuven.be] QSAR / QSPR data mining software package DMax Chemistry Assistant is now a free download, no need to register anymore. Useful for: 1. Find and display target-correlated and anti-correlated graph patterns at atom-bond level, functional group level, and mixed. 2. Build a predictive QSPR / QSAR model. (The built-in machine learning algorithms are not the strongest available, but you get an explanation for each decision.) 3. Export features for use in other tools. 4. Functional group detection. It creates a Prolog file that is easy to read. This can improve the predictive accuracy of other tools. http://dtai.cs.kuleuven.be/dmax/ Kurt. -- Dr. ir. Kurt De Grave http://dtai.cs.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Tue Sep 3 07:24:00 2013 From: "Francisco Adasme fadasmec- -utalca.cl" To: CCL Subject: CCL:G: How to visualize the ESP of a single molecule inside a bigger system Message-Id: <-49133-130902234922-16667-n6hk07nQXXkmWmfQTc0EAQ:server.ccl.net> X-Original-From: "Francisco Adasme" Date: Mon, 2 Sep 2013 23:49:21 -0400 Sent to CCL by: "Francisco Adasme" [fadasmec],[utalca.cl] Hi, I am currently trying to study how certain amino acids affect the strength of a hydrogen bond occurring in the binding site of a known protein. To address this, I proposed to calculate the electrostatic potential (ESP) surface of the two interacting molecules through DFT calculations in several systems, where one each of them includes an increasing number of surrounding amino acids' sidechains. Preliminary results indicate that it's indeed possible to detect subtle changes in the ESP of organic molecules using this type of calculation. However, none of the literature I have read so far shows the calculation nor visualisation of the ESP of a single molecule in a many-molecule system (like the aforementioned), so I was wondering whether it's possible and how to do it, since my first attempts in doing so have failed (I have used Gaussian and Gaussian View, USCF Chimera and Avogrado visualisation software) inasmuch as I only obtained an enclosing surface of the entire system, therefore I cannot see the changes at the regions where the interaction occurs. I hope you can enlighten me in this regard, since I'm new to this kind of calculations. Thanks. From owner-chemistry@ccl.net Tue Sep 3 08:42:01 2013 From: "sobereva~~sina.com" To: CCL Subject: CCL: How to visualize the ESP of a single molecule inside a bigger system Message-Id: <-49134-130903083312-15777-WwyaGV/ahFohug0Mzf94xw()server.ccl.net> X-Original-From: Content-Type: multipart/alternative; boundary="=-sinamail_alt_0ce77933afbe740e5f848320655f3a0c" Date: Tue, 03 Sep 2013 20:32:55 +0800 MIME-Version: 1.0 Sent to CCL by: [sobereva * sina.com] --=-sinamail_alt_0ce77933afbe740e5f848320655f3a0c Content-Type: text/plain; charset=GBK Content-Transfer-Encoding: base64 Content-Disposition: inline SGksDQogDQpIYXZlIGEgbG9vayBhdCBDcnlzdEVuZ0NvbW0sIDIwMDksIDExLCAxOS0zMiwgdGhl IEhpcnNoZmVsZCBzdXJmYWNlIGFuYWx5c2lzIGRlc2NyaWJlZCBpbiB0aGlzIHBhcGVyIGlzIGEg bmljZSBpZGVhIHRvIGNvbnN0cnVjdCB0aGUgc3VyZmFjZSBvZiBhIHNpbmdsZSBtb2xlY3VsZSBp biBjb21wbGV4IG9yIGluIG1vbGVjdWxhciBjcnlzdGFsLiBZb3UgY2FuIHN0dWR5IHRoZSBFU1Ag ZGlzdHJpYnV0aW9uIG9uIHRoZSBjb3JyZXNwb25kaW5nIEhpcnNoZmVsZCBzdXJmYWNlLg0KIA0K QmVzdCB3aXNoZXMsDQogDQpUaWFuIEx1CgoNCg0KLS0tLS0gT3JpZ2luYWwgTWVzc2FnZSAtLS0t LQpGcm9tOiAiRnJhbmNpc2NvIEFkYXNtZSBmYWRhc21lYy0gLXV0YWxjYS5jbCIgPG93bmVyLWNo ZW1pc3RyeUBjY2wubmV0PgpUbzogIkx1LCBUaWFuIC1pZCMzcGgtIiA8c29iZXJldmFAc2luYS5j b20+ClN1YmplY3Q6IENDTDpHOiBIb3cgdG8gdmlzdWFsaXplIHRoZSBFU1Agb2YgYSBzaW5nbGUg bW9sZWN1bGUgaW5zaWRlIGEgYmlnZ2VyIHN5c3RlbQpEYXRlOiAyMDEzLTA5LTAzIDExOjQ5CgoK U2VudCB0byBDQ0wgYnk6ICJGcmFuY2lzY28gQWRhc21lIiBbZmFkYXNtZWNdLFt1dGFsY2EuY2xd CkhpLApJIGFtIGN1cnJlbnRseSB0cnlpbmcgdG8gc3R1ZHkgaG93IGNlcnRhaW4gYW1pbm8gYWNp ZHMgYWZmZWN0IHRoZSBzdHJlbmd0aCBvZiBhIGh5ZHJvZ2VuIGJvbmQgb2NjdXJyaW5nIAppbiB0 aGUgYmluZGluZyBzaXRlIG9mIGEga25vd24gcHJvdGVpbi4gVG8gYWRkcmVzcyB0aGlzLCBJIHBy b3Bvc2VkIHRvIGNhbGN1bGF0ZSB0aGUgZWxlY3Ryb3N0YXRpYyAKcG90ZW50aWFsIChFU1ApIHN1 cmZhY2Ugb2YgdGhlIHR3byBpbnRlcmFjdGluZyBtb2xlY3VsZXMgdGhyb3VnaCBERlQgY2FsY3Vs YXRpb25zIGluIHNldmVyYWwgc3lzdGVtcywgCndoZXJlIG9uZSBlYWNoIG9mIHRoZW0gaW5jbHVk ZXMgYW4gaW5jcmVhc2luZyBudW1iZXIgb2Ygc3Vycm91bmRpbmcgYW1pbm8gYWNpZHMnIHNpZGVj aGFpbnMuClByZWxpbWluYXJ5IHJlc3VsdHMgaW5kaWNhdGUgdGhhdCBpdCdzIGluZGVlZCBwb3Nz aWJsZSB0byBkZXRlY3Qgc3VidGxlIGNoYW5nZXMgaW4gdGhlIEVTUCBvZiBvcmdhbmljIAptb2xl Y3VsZXMgdXNpbmcgdGhpcyB0eXBlIG9mIGNhbGN1bGF0aW9uLiBIb3dldmVyLCBub25lIG9mIHRo ZSBsaXRlcmF0dXJlIEkgaGF2ZSByZWFkIHNvIGZhciBzaG93cyB0aGUgCmNhbGN1bGF0aW9uIG5v ciB2aXN1YWxpc2F0aW9uIG9mIHRoZSBFU1Agb2YgYSBzaW5nbGUgbW9sZWN1bGUgaW4gYSBtYW55 LW1vbGVjdWxlIHN5c3RlbSAobGlrZSB0aGUgCmFmb3JlbWVudGlvbmVkKSwgc28gSSB3YXMgd29u ZGVyaW5nIHdoZXRoZXIgaXQncyBwb3NzaWJsZSBhbmQgaG93IHRvIGRvIGl0LCBzaW5jZSBteSBm aXJzdCBhdHRlbXB0cyBpbiAKZG9pbmcgc28gaGF2ZSBmYWlsZWQgKEkgaGF2ZSB1c2VkIEdhdXNz aWFuIGFuZCBHYXVzc2lhbiBWaWV3LCBVU0NGIENoaW1lcmEgYW5kIEF2b2dyYWRvIAp2aXN1YWxp c2F0aW9uIHNvZnR3YXJlKSBpbmFzbXVjaCBhcyBJIG9ubHkgb2J0YWluZWQgYW4gZW5jbG9zaW5n IHN1cmZhY2Ugb2YgdGhlIGVudGlyZSBzeXN0ZW0sIHRoZXJlZm9yZSAKSSBjYW5ub3Qgc2VlIHRo ZSBjaGFuZ2VzIGF0IHRoZSByZWdpb25zIHdoZXJlIHRoZSBpbnRlcmFjdGlvbiBvY2N1cnMuCkkg aG9wZSB5b3UgY2FuIGVubGlnaHRlbiBtZSBpbiB0aGlzIHJlZ2FyZCwgc2luY2UgSSdtIG5ldyB0 byB0aGlzIGtpbmQgb2YgY2FsY3VsYXRpb25zLgpUaGFua3MuCi09IFRoaXMgaXMgYXV0b21hdGlj YWxseSBhZGRlZCB0byBlYWNoIG1lc3NhZ2UgYnkgdGhlIG1haWxpbmcgc2NyaXB0ID0tClRvIHJl Y292ZXIgdGhlIGVtYWlsIGFkZHJlc3Mgb2YgdGhlIGF1dGhvciBvZiB0aGUgbWVzc2FnZSwgcGxl YXNlIGNoYW5nZQp0aGUgc3RyYW5nZSBjaGFyYWN0ZXJzIG9uIHRoZSB0b3AgbGluZSB0byB0aGUg QCBzaWduLiBZb3UgY2FuIGFsc28KbG9vayB1cCB0aGUgWC1PcmlnaW5hbC1Gcm9tOiBsaW5lIGlu IHRoZSBtYWlsIGhlYWRlci4KRS1tYWlsIHRvIHN1YnNjcmliZXJzOiBDSEVNSVNUUllAY2NsLm5l dCBvciB1c2U6Cmh0dHA6Ly93d3cuY2NsLm5ldC9jZ2ktYmluL2NjbC9zZW5kX2NjbF9tZXNzYWdl CkUtbWFpbCB0byBhZG1pbmlzdHJhdG9yczogQ0hFTUlTVFJZLVJFUVVFU1RAY2NsLm5ldCBvciB1 c2UKaHR0cDovL3d3dy5jY2wubmV0L2NnaS1iaW4vY2NsL3NlbmRfY2NsX21lc3NhZ2UKU3Vic2Ny aWJlL1Vuc3Vic2NyaWJlOiAKaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9zdWJfdW5zdWIu c2h0bWwKQmVmb3JlIHBvc3RpbmcsIGNoZWNrIHdhaXQgdGltZSBhdDogaHR0cDovL3d3dy5jY2wu bmV0CkpvYjogaHR0cDovL3d3dy5jY2wubmV0L2pvYnMgCkNvbmZlcmVuY2VzOiBodHRwOi8vc2Vy dmVyLmNjbC5uZXQvY2hlbWlzdHJ5L2Fubm91bmNlbWVudHMvY29uZmVyZW5jZXMvClNlYXJjaCBN ZXNzYWdlczogaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9zZWFyY2hjY2wvaW5kZXguc2h0 bWwKSWYgeW91ciBtYWlsIGJvdW5jZXMgZnJvbSBDQ0wgd2l0aCA1LjcuMSBlcnJvciwgY2hlY2s6 Cmh0dHA6Ly93d3cuY2NsLm5ldC9zcGFtbWVycy50eHQKUlRGSTogaHR0cDovL3d3dy5jY2wubmV0 L2NoZW1pc3RyeS9hYm91dGNjbC9pbnN0cnVjdGlvbnMvCg== --=-sinamail_alt_0ce77933afbe740e5f848320655f3a0c Content-Type: text/html; 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charset=ISO-8859-1; format=flowed Date: Tue, 03 Sep 2013 15:13:45 +0200 MIME-Version: 1.0 Sent to CCL by: Kurt De Grave [Kurt.DeGrave_-_cs.kuleuven.be] On 09/03/2013 09:33 AM, Kurt De Grave Kurt.DeGrave%x%cs.kuleuven.be wrote: > QSAR / QSPR data mining software package DMax Chemistry Assistant is now > a free download, no need to register anymore. > > Useful for: > 1. Find and display target-correlated and anti-correlated graph patterns > at atom-bond level, functional group level, and mixed. > 2. Build a predictive QSPR / QSAR model. (The built-in machine learning > algorithms are not the strongest available, but you get an explanation > for each decision.) > 3. Export features for use in other tools. > 4. Functional group detection. It creates a Prolog file that is easy to > read. This can improve the predictive accuracy of other tools. > > http://dtai.cs.kuleuven.be/dmax/ There was unfortunately a problem for the 64-bit Windows OS, which has now been fixed thanks to helpful bug reports. If you ran into trouble, try the new build. kurt. -- Dr. ir. Kurt De Grave http://dtai.cs.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm From owner-chemistry@ccl.net Tue Sep 3 12:24:00 2013 From: "Brian Jay Levandowski levandbj|a|plu.edu" To: CCL Subject: CCL:G: Transition State TS Berry Optimization Message-Id: <-49136-130903112026-22866-tzUvlY4xPM3gxW5NoWghiQ:_:server.ccl.net> X-Original-From: "Brian Jay Levandowski" Date: Tue, 3 Sep 2013 11:20:25 -0400 Sent to CCL by: "Brian Jay Levandowski" [levandbj{}plu.edu] Hello, I am running a TS Berry optimization with B3LYP 6-31+G. When the optimization converges (after many iterations) the output geometry is a mess.My input geometry is my best guess from minimizing the reactant then elongated the bond to 2.1 angstroms. I then froze the bond at 2.1 angstroms and did another minimization optimization to get my input geometry for the TS search. In looking at the TS search intermediate gemoetries, intitially it looks like it is headed to the TS and possibly converging, but then it jumps to the reactant and the energy spikes way up. It then heads downhill and converges to a TS involving a C-C bond breaking instead of the C-O bond I initially elongated. My questions are: 1. I took one of the intermediate geometries that looked like what I would expect the intermediate to look like and ran an IRC on it. It lead to the reactant and an intermediate, but it was not a true TS (second derivative) from the TS Berry search as it did not converge on that geometry. So is it not the TS I am looking for? 2. Could I constrain/freeze the C-C bond that is being broken in my TS Berry optimization to prevent the spike from happening where it enters weird geometries? Or do constraints make the system to artificial. 3. I would also like to if it is possibly to modify how much the bond length increases and each step in which a calculation is done. In my optimization the C-O bond starts at 2.1 then jumps to 2.35, 2.58, 2.83... hits 3.85 then goes back down eventually to 2.49 (this is where I think the TS is, but it never converges) then continues to 1.44 which is the bond length in the reactant then is spikes and goes askew as mentioned above. Should I try and scan the distance of the C-O bond from say 1.85 to around 3.0 in increments of 0.1 angstroms? If so should I also constrain all the other variables or does a scan constrain everything but the variables being manipulated? Any pointers/resources on finding TS with gaussian would also be helpful. I am an undergrad interested in going to grad. school for computational chemistry. I've used Lewar's computational chemistry but it would be great if there was a guide more specific to gaussview/gaussian. Thank you, Brian Levandowski levandbj-$-plu.edu From owner-chemistry@ccl.net Tue Sep 3 12:59:00 2013 From: "David Gallagher gallagher.da---gmail.com" To: CCL Subject: CCL: Workshop (update): Next Gen. MM & QSAR, Indianapolis ACS, 9/10/13 Message-Id: <-49137-130903121635-27542-NXiF5WPR9HXwNjj9BqvbrQ++server.ccl.net> X-Original-From: David Gallagher Content-Type: multipart/alternative; boundary="------------020208090508010109090502" Date: Tue, 03 Sep 2013 09:16:27 -0700 MIME-Version: 1.0 Sent to CCL by: David Gallagher [gallagher.da^gmail.com] This is a multi-part message in MIME format. --------------020208090508010109090502 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit *Workshop:Next Generation Molecular Modeling & QSAR *Presenter:Prof. Tim Clark Time:6pm - 7.30pm, Tuesday 10th September 2013 Venue:Indiana University-Purdue University Indianapolis Campus, IN, USA LD Building (click for map) , *Room 326T (third floor*) (15 minutes walk from the ACS exposition hall)* *Web-site:http://www.cacheresearch.com/aiche.html#training * Background and introduction: *ProfessorTim Clark (University of Erlangen, Germany) will start by providing an introduction to two next-generation molecular modeling tools. "SAR-caddle " is a web-based tool for building & applying robust QSAR/QSPR models with applicability domain analysis & 3D visualization, and "EMPIRE-caddle " is a web-based QM molecular modeling system with advanced flexible workflows and protocols, and interactive 3D-visualization that is ideally suited for teaching and research. These new tools require only a suitable browser on a desktop computer, laptop, tablet or smart phone (no local installation).* Hands-on training session: *This will be followed by a hands-on training session with SAR-caddle & EMPIRE-caddle, so please bring your own laptop or tablet. No software installation is necessary as the tools are all web-based. A web server with local wireless LAN will make the software available. Recommended browsers are Chrome or Firefox under Windows and Safari on Macs. *Registration:* The workshop is free but seats are limited so please send your registration toWorkshop.:.CACheResearch.com , and include name, affiliation, and location, or register at Booth 534 at the ACS Exposition. --------------020208090508010109090502 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Workshop:       Next Generation Molecular Modeling & QSAR
Presenter:         Prof. Tim Clark
Time:                6pm - 7.30pm, Tuesday 10th September 2013
Venue:              Indiana University-Purdue University Indianapolis Campus, IN, USA
                        LD Building (click for map), Room 326T (third floor)
                        (15 minutes walk from the ACS exposition hall)
Web-site:          http://www.cacheresearch.com/aiche.html#training
Background and introduction:  
Professor Tim Clark (University of Erlangen, Germany) will start by providing an introduction to two next-generation molecular modeling tools. "SAR-caddle" is a web-based tool for building & applying robust QSAR/QSPR models with applicability domain analysis & 3D visualization, and "EMPIRE-caddle" is a web-based QM molecular modeling system with advanced flexible workflows and protocols, and interactive 3D-visualization that is ideally suited for teaching and research.  These new tools require only a suitable browser on a desktop computer, laptop, tablet or smart phone (no local installation).

Hands-on training session:  
This will be followed by a hands-on training session with SAR-caddle & EMPIRE-caddle, so please bring your own laptop or tablet.  No software installation is necessary as the tools are all web-based. A web server with local wireless LAN will make the software available.  Recommended browsers are Chrome or Firefox under Windows and Safari on Macs.

Registration:  The workshop is free but seats are limited so please send your registration to Workshop.:.CACheResearch.com, and include name, affiliation, and location, or register at Booth 534 at the ACS Exposition. --------------020208090508010109090502-- From owner-chemistry@ccl.net Tue Sep 3 13:34:00 2013 From: "John Keller jwkeller!^!alaska.edu" To: CCL Subject: CCL:G: Transition State TS Berry Optimization Message-Id: <-49138-130903131512-31737-NQqOexXrVhkSOhmGQn1dzw|a|server.ccl.net> X-Original-From: John Keller Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 3 Sep 2013 09:15:03 -0800 Mime-Version: 1.0 (1.0) Sent to CCL by: John Keller [jwkeller*|*alaska.edu] Brian, Your level of theory is too low. Try more stars, then another + John Keller Univ of Alaska Fairbanks Sent from my iPad On Sep 3, 2013, at 8:56 AM, "Brian Jay Levandowski levandbj|a|plu.edu" wrote: > > Sent to CCL by: "Brian Jay Levandowski" [levandbj{}plu.edu] > Hello, > > I am running a TS Berry optimization with B3LYP 6-31+G. When the optimization converges (after > many iterations) the output geometry is a mess.My input geometry is my best guess from > minimizing the reactant then elongated the bond to 2.1 angstroms. I then froze the bond at 2.1 > angstroms and did another minimization optimization to get my input geometry for the TS search. > > In looking at the TS search intermediate gemoetries, intitially it looks like it is headed to the TS and > possibly converging, but then it jumps to the reactant and the energy spikes way up. It then heads > downhill and converges to a TS involving a C-C bond breaking instead of the C-O bond I initially > elongated. > > My questions are: > 1. I took one of the intermediate geometries that looked like what I would expect the intermediate > to look like and ran an IRC on it. It lead to the reactant and an intermediate, but it was not a true TS > (second derivative) from the TS Berry search as it did not converge on that geometry. So is it not the > TS I am looking for? > > 2. Could I constrain/freeze the C-C bond that is being broken in my TS Berry optimization to > prevent the spike from happening where it enters weird geometries? Or do constraints make the > system to artificial. > > 3. I would also like to if it is possibly to modify how much the bond length increases and each step > in which a calculation is done. In my optimization the C-O bond starts at 2.1 then jumps to 2.35, > 2.58, 2.83... hits 3.85 then goes back down eventually to 2.49 (this is where I think the TS is, but it > never converges) then continues to 1.44 which is the bond length in the reactant then is spikes and > goes askew as mentioned above. Should I try and scan the distance of the C-O bond from say 1.85 > to around 3.0 in increments of 0.1 angstroms? If so should I also constrain all the other variables or > does a scan constrain everything but the variables being manipulated? > > Any pointers/resources on finding TS with gaussian would also be helpful. I am an undergrad > interested in going to grad. school for computational chemistry. I've used Lewar's computational > chemistry but it would be great if there was a guide more specific to gaussview/gaussian. > > Thank you, > Brian Levandowski > levandbj],[plu.edu> > From owner-chemistry@ccl.net Tue Sep 3 14:20:00 2013 From: "Juan Manuel Arce mayerzmytm()gmail.com" To: CCL Subject: CCL: unresolvable inconsistency in Gaussian Message-Id: <-49139-130903135739-14973-WX+Gj2xr7YtQDCsHIKW0fQ]=[server.ccl.net> X-Original-From: "Juan Manuel Arce" Date: Tue, 3 Sep 2013 13:57:38 -0400 Sent to CCL by: "Juan Manuel Arce" [mayerzmytm]=[gmail.com] Hello all, Im optimizing some structures involving hydrocarbons and metal atoms (specifically for adsorption purposes), but in some of them I get the message: "unresolvable inconsistency between charge and multiplicity and orbital occupancies. Orbital data will be ignored" Does this means that the energy I get from this file would be wrong. If I am only interested in doing reaction pathway calculation, involving transition states configurations, can I take the energy hoping no error? hope that anybody can help best regards, Juan Manuel Arce From owner-chemistry@ccl.net Tue Sep 3 16:28:00 2013 From: "Dan Maftei dan.maftei()uaic.ro" To: CCL Subject: CCL: Transition State TS Berry Optimization Message-Id: <-49140-130903161605-17887-+vylA6+JLTkZrey/vSKEhg!A!server.ccl.net> X-Original-From: Dan Maftei Content-Type: multipart/alternative; boundary="--_com.android.email_72308756669470" Date: Tue, 03 Sep 2013 23:15:49 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei!=!uaic.ro] ----_com.android.email_72308756669470 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: base64 RGVhciBCcmlhbiwKClRoZSBmb2xsb3dpbmcgY29uc2lkZXJhdGlvbiBtaWdodCBoZWxwOiBUUyBp bnZvbHZlcyBub3Qgb25seSBhIGJvbmQgYnJlYWtpbmcsIGJ1dCBhbHNvIGEgbmV3IGJvbmQgdGhh dCBpcyBmb3JtZWQgZHVyaW5nIHRoYXQgcmVhY3Rpb24gc3RlcC4gVGhlIHNhZGRsZSBwb2ludCBu 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Y2s6PGJyPiZuYnNwOyZuYnNwOyZuYnNwOyZuYnNwOyZuYnNwOyBodHRwOi8vd3d3LmNjbC5uZXQv c3BhbW1lcnMudHh0PGJyPjxicj5SVEZJOiBodHRwOi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L2Fi b3V0Y2NsL2luc3RydWN0aW9ucy88YnI+PGJyPjxicj4gPC9ib2R5Pg== ----_com.android.email_72308756669470-- From owner-chemistry@ccl.net Tue Sep 3 17:22:00 2013 From: "Radoslaw Kaminski rkaminski.rk:+:gmail.com" To: CCL Subject: CCL:G: How to visualize the ESP of a single molecule inside a bigger system Message-Id: <-49141-130903093108-8775-2vGP9xSDdykErxznrQ88Lw^^server.ccl.net> X-Original-From: Radoslaw Kaminski Content-Type: multipart/alternative; boundary=047d7b66fc0f214f0c04e57ab3db Date: Tue, 3 Sep 2013 09:30:20 -0400 MIME-Version: 1.0 Sent to CCL by: Radoslaw Kaminski [rkaminski.rk^gmail.com] --047d7b66fc0f214f0c04e57ab3db Content-Type: text/plain; charset=ISO-8859-1 Hello, Mentioned Hirshfeld surfaces are indeed a very good choice. However, you have to keep in mind what ESP you will map onto the surface. Original Spackman idea was to take an isolated molecule ESP and map it onto the Hirshfeld surface. I once checked what is the difference if you take ESP for whole system. The oveall ESP features on the surface are indeed significantly different (complementary regions vanish etc.). Depends on what you what to learn and what to show. Best wishes, Radek On 3 September 2013 08:32, sobereva~~sina.com wrote: > Hi, > > Have a look at CrystEngComm, 2009, 11, 19-32, the Hirshfeld surface > analysis described in this paper is a nice idea to construct the surface of > a single molecule in complex or in molecular crystal. You can study the ESP > distribution on the corresponding Hirshfeld surface. > > Best wishes, > > Tian Lu > > ----- Original Message ----- > From: "Francisco Adasme fadasmec- -utalca.cl" > To: "Lu, Tian " > Subject: CCL:G: How to visualize the ESP of a single molecule inside a > bigger system > Date: 2013-09-03 11:49 > > > Sent to CCL by: "Francisco Adasme" [fadasmec],[utalca.cl] > Hi, > I am currently trying to study how certain amino acids affect the strength > of a hydrogen bond occurring > in the binding site of a known protein. To address this, I proposed to > calculate the electrostatic > potential (ESP) surface of the two interacting molecules through DFT > calculations in several systems, > where one each of them includes an increasing number of surrounding amino > acids' sidechains. > Preliminary results indicate that it's indeed possible to detect subtle > changes in the ESP of organic > molecules using this type of calculation. However, none of the literature > I have read so far shows the > calculation nor visualisation of the ESP of a single molecule in a > many-molecule system (like the > aforementioned), so I was wondering whether it's possible and how to do > it, since my first attempts in > doing so have failed (I have used Gaussian and Gaussian View, USCF Chimera > and Avogrado > visualisation software) inasmuch as I only obtained an enclosing surface > of the entire system, therefore > I cannot see the changes at the regions where the interaction occurs. > I hope you can enlighten me in this regard, since I'm new to this kind of > calculations. > Thanks.> -- Radoslaw Kaminski, Ph.D. Eng. Postdoctoral Research Associate Department of Chemistry, University at Buffalo The State University of New York 747 Natural Sciences Complex Buffalo, NY 14260-3000, USA http://www.chem.uw.edu.pl/people/RKaminski/ --047d7b66fc0f214f0c04e57ab3db Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hello,

Mentioned Hirshfeld surfaces are indeed= a very good choice. However, you have to keep in mind what ESP you will ma= p onto the surface. Original Spackman idea was to take an isolated molecule= ESP and map it onto the Hirshfeld surface. I once checked what is the diff= erence if you take ESP for whole system. The oveall ESP features on the sur= face are indeed significantly different (complementary regions vanish etc.)= . Depends on what you what to learn and what to show.

Best wishes,

Radek



On 3 September 20= 13 08:32, sobereva~~sina.com <owner-= chemistry.:.ccl.net> wrote:
Hi,
=A0
Have a look at=A0CrystEngComm, 2009, 11, 19-32,=A0the Hirshfeld surfac= e analysis described in this paper is a nice idea to construct the surface = of a single molecule in complex or in molecular crystal. You can study the = ESP distribution on the corresponding=A0Hirshfeld surface.
=A0
Best wishes,
=A0
Tian Lu

----- Original Message -----
From: &qu= ot;Francisco Adasme fadasmec- -utalca.cl" <owner-chemistry.:.ccl.net>
To: "Lu, Tian " <sobereva.:.sina.com>
Subject: CCL:G: How to visua= lize the ESP of a single molecule inside a bigger system
Date: 2013-09-0= 3 11:49


Sent to CCL by: "Francisco Adasme" [fadasmec],[utalca.cl]
Hi,
I am cu= rrently trying to study how certain amino acids affect the strength of a hy= drogen bond occurring
in the binding site of a known protein. To address this, I proposed to calc= ulate the electrostatic
potential (ESP) surface of the two interacting = molecules through DFT calculations in several systems,
where one each o= f them includes an increasing number of surrounding amino acids' sidech= ains.
Preliminary results indicate that it's indeed possible to detect subtle= changes in the ESP of organic
molecules using this type of calculation= . However, none of the literature I have read so far shows the
calculat= ion nor visualisation of the ESP of a single molecule in a many-molecule sy= stem (like the
aforementioned), so I was wondering whether it's possible and how to do= it, since my first attempts in
doing so have failed (I have used Gauss= ian and Gaussian View, USCF Chimera and Avogrado
visualisation software= ) inasmuch as I only obtained an enclosing surface of the entire system, th= erefore
I cannot see the changes at the regions where the interaction occurs.
I = hope you can enlighten me in this regard, since I'm new to this kind of= calculations.
Thanks.
-=3D This is automatically added to each messa= ge by the mailing script =3D-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_message
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--
Rad= oslaw Kaminski, Ph.D. Eng.
Postdoctoral Research Associate
Department of Chemistry, University at B= uffalo
The State University of New York
747 Natural Sciences Complex =
Buffalo, NY 14260-3000, USA
http://www.chem.uw.edu.pl/people/RKamin= ski/
--047d7b66fc0f214f0c04e57ab3db-- From owner-chemistry@ccl.net Tue Sep 3 17:56:00 2013 From: "Salter-Duke, Brian James - brian.james.duke_._gmail.com" To: CCL Subject: CCL: unresolvable inconsistency in Gaussian Message-Id: <-49142-130903172609-13548-kV+a7wlTQwQj6ExW2YdOMw-x-server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 4 Sep 2013 07:25:52 +1000 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke~!~gmail.com] On Tue, Sep 03, 2013 at 01:57:38PM -0400, Juan Manuel Arce mayerzmytm()gmail.com wrote: > > Sent to CCL by: "Juan Manuel Arce" [mayerzmytm]=[gmail.com] > Hello all, > > Im optimizing some structures involving hydrocarbons and metal atoms > (specifically for adsorption purposes), but in some of them I get the message: > > "unresolvable inconsistency between charge and multiplicity and orbital > occupancies. Orbital data will be ignored" > > Does this means that the energy I get from this file would be wrong. If I am > only interested in doing reaction pathway calculation, involving transition > states configurations, can I take the energy hoping no error? It looks like you have a real problem. It could be that either an orbital degeneracy has been broken, or that some orbitals have moved to be degenerate. It depends on the system, but either way the multiplicity would change and you would get an inconsistency. Does this make sense. Without knowing the molecule, and the state you are looking at, or indeed the program you are using, it is difficult to be more specific. Brian. > hope that anybody can help > > best regards, > > Juan Manuel Arce> -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke:-:monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Tue Sep 3 18:43:00 2013 From: "Peter Buger burger:chemie.uni-hamburg.de" To: CCL Subject: CCL: patchfile for Intel compiler for G09 D01 Message-Id: <-49143-130903170630-3851-kA2U2+UB58vkw0xv7erUpw**server.ccl.net> X-Original-From: "Peter Buger" Date: Tue, 3 Sep 2013 17:06:28 -0400 Sent to CCL by: "Peter Buger" [burger(~)chemie.uni-hamburg.de] Dear CCLers, anyone would like to share a patchfile for compiling g09_D01 with Intels ifort compiler with me? It will stay with me. Thanks in advance! Cheers Peter From owner-chemistry@ccl.net Tue Sep 3 19:18:01 2013 From: "Juan Manuel mayerzmytm*gmail.com" To: CCL Subject: CCL:G: unresolvable inconsistency in Gaussian Message-Id: <-49144-130903185204-14017-ZlLG8+3i/zkcc2q/4Rt7GQ%a%server.ccl.net> X-Original-From: Juan Manuel Content-Type: multipart/alternative; boundary=001a11c2ff223ca34c04e582893d Date: Tue, 3 Sep 2013 17:51:37 -0500 MIME-Version: 1.0 Sent to CCL by: Juan Manuel [mayerzmytm]~[gmail.com] --001a11c2ff223ca34c04e582893d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Thanks for answer Brian, I=B4m using Gaussian09 for the calculations, I=B4m adsorbing ethane over a = Pd cluster, that according in what I reviewed should be triplet (the Pd cluster) to accelerate the process I=B4m doing a ONIOM calculation with a fast basis set for Pd atoms (LANL2DZ) and 6-31g(d,p) for lighter atoms with the B3LYP functional. Could the ONIOM be the responsable for that error? best regards, Juan Manuel 2013/9/3 Salter-Duke, Brian James brian.james.duke_._gmail.com < owner-chemistry a ccl.net> > > Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke~!~ > gmail.com] > On Tue, Sep 03, 2013 at 01:57:38PM -0400, Juan Manuel Arce mayerzmytm() > gmail.com wrote: > > > > Sent to CCL by: "Juan Manuel Arce" [mayerzmytm]=3D[gmail.com] > > Hello all, > > > > Im optimizing some structures involving hydrocarbons and metal atoms > > (specifically for adsorption purposes), but in some of them I get the > message: > > > > "unresolvable inconsistency between charge and multiplicity and orbital > > occupancies. Orbital data will be ignored" > > > > Does this means that the energy I get from this file would be wrong. If > I am > > only interested in doing reaction pathway calculation, involving > transition > > states configurations, can I take the energy hoping no error? > > It looks like you have a real problem. It could be that either an > orbital degeneracy has been broken, or that some orbitals have moved to > be degenerate. It depends on the system, but either way the multiplicity > would change and you would get an inconsistency. Does this make sense. > Without knowing the molecule, and the state you are looking at, or > indeed the program you are using, it is difficult to be more specific. > > Brian. > > > hope that anybody can help > > > > best regards, > > > > Juan Manuel Arce> > > -- > Brian Salter-Duke (Brian Duke) Brian.Salter-Duke(0)monash.edu > Adjunct Associate Professor > Monash Institute of Pharmaceutical Sciences > Monash University Parkville Campus, VIC 3052, Australia > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 ********************************************************* I.Q. Juan Manuel Arce Ramos Facultad de Ciencias Qu=EDmicas Universidad Aut=F3noma de San Luis Potos=ED Tel:(444)8262440 ext 543 * ********************************************************** --001a11c2ff223ca34c04e582893d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Thanks for answer Brian,

I=B4m using Ga= ussian09 for the calculations, I=B4m adsorbing ethane over a Pd cluster, th= at according in what I reviewed should be triplet (the Pd cluster)

to accelerate the process I=B4m doing a ONIOM calculation with a= fast basis set for Pd atoms (LANL2DZ) and 6-31g(d,p) for lighter atoms wit= h the B3LYP functional. Could the ONIOM be the responsable for that error?<= /div>

best regards,

Juan Manuel


2013/9= /3 Salter-Duke, Brian James brian.james.duke_._gmail.com <owner-chemistry a ccl.net>

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke~!~gmail.com]
On Tue, Sep 03, 2013 at 01:57:38PM -0400, Juan Manuel Arc= e mayerzmytm()gmail.com = wrote:
>
> Sent to CCL by: "Juan Manuel Arce" [mayerzmytm]=3D[gmail.com]
> Hello all,
>
> Im optimizing some structures involving hydrocarbons and metal atoms > (specifically for adsorption purposes), but in some of them I get the = message:
>
> "unresolvable inconsistency between charge and multiplicity and o= rbital
> occupancies. Orbital data will be ignored"
>
> Does this means that the energy I get from this file would be wrong. I= f I am
> only interested in doing reaction pathway calculation, involving trans= ition
> states configurations, can I take the energy hoping no error?

It looks like you have a real problem. It could be that either an
orbital degeneracy has been broken, or that some orbitals have moved to
be degenerate. It depends on the system, but either way the multiplicity would change and you would get an inconsistency. Does this make sense.
Without knowing the molecule, and the state you are looking at, or
indeed the program you are using, it is difficult to be more specific.

Brian.

> hope that anybody can help
>
> best regards,
>
> Juan Manuel Arce>

--
=A0 =A0Brian Salter-Duke (Brian Duke) =A0 Brian.Salter-Duke(0)monash.edu
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Adjunct Associate Professor
=A0 =A0 =A0 =A0 =A0 =A0 Monash Institute of Pharmaceutical Sciences
=A0 =A0 =A0 Monash University Parkville Campus, VIC 3052, Australia



-=3D This is automatically added to each message by the mailing script =3D-=
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--
= 
********************************************************
I.Q. Juan Manuel Arce Ramos
 Facultad de Ciencias Qu=EDmicas
  Universidad Aut=F3noma de San Luis Potos=ED
 Tel:=
(444)8262440 ext 543
**************************=
******************************

--001a11c2ff223ca34c04e582893d-- From owner-chemistry@ccl.net Tue Sep 3 19:53:01 2013 From: "Mark Zottola mzottola._._.gmail.com" To: CCL Subject: CCL:G: Dipole Moment Calculation within Gaussian Message-Id: <-49145-130903185628-17244-tZCtUwPsqlQZnj1ezr5kaA_._server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=047d7b343eca00777904e58299f4 Date: Tue, 3 Sep 2013 18:56:21 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola{}gmail.com] --047d7b343eca00777904e58299f4 Content-Type: text/plain; charset=ISO-8859-1 Thanks for sharing this. As I am interested in how certain functional groups within a molecule align wrt the molecular dipole, this does allow me the confidence to know my methodology is correct. Cina had said surmised this hard to be true in a private communication to me. In any case, thanks to all who have responded. It is appreciated! Mark On Mon, Sep 2, 2013 at 8:28 PM, Salter-Duke, Brian James brian.james.duke[]gmail.com wrote: > > Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke:_: > gmail.com] > On Mon, Sep 02, 2013 at 11:58:08AM -0400, Mark Zottola mzottola(-) > gmail.com wrote: > > Are the cartesian components of the dipole moment shown in the gaussian > > output based on a center of mass, center of charge, or geometric center > for > > the origin? If the last, is that based on the "Input Orientation" or the > > "Standard Orientation"? > > > > I did not find this info when I dove Gaussian's web pages nor a simple > > google search. Any help would be greatly appreciated. > > I got an answer to this exact question from Gaussian only last week. The > dipole integrals are evaluated with whatever origin Gaussian is using > for the coordinates . These are normally the "Standard Orientation" > coordinates and these are based on the origin at the centre of charge. > There is an IOP code to use the centre of mass. > > As another poster has said, this does not affect the dipole moment, but > it defines the x, y, z axis for the cartesian components. > > Brian. > > > Thanks, > > > > > > Mark > > -- > Brian Salter-Duke (Brian Duke) Brian.Salter-Duke:+:monash.edu > Adjunct Associate Professor > Monash Institute of Pharmaceutical Sciences > Monash University Parkville Campus, VIC 3052, Australia> > > --047d7b343eca00777904e58299f4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Thanks for sharing this. =A0As I am interested in how cert= ain functional groups within a molecule align wrt the molecular dipole, thi= s does allow me the confidence to know my methodology is correct.

<= /div>
Cina had said surmised this hard to be true in a private communication= to me. =A0In any case, =A0thanks to all who have responded. =A0It is appre= ciated!


Mark


On Mon, Sep 2, 2013 at 8:28 PM, Salter-D= uke, Brian James brian.james.duke[]gm= ail.com <owner-chemistry _ ccl.net> wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke:_:gmail.com]
On Mon, Sep 02, 2013 at 11:58:08AM -0400, Mark Zottola mzottola(-)gmail.com wrote:
> Are the cartesian components of the dipole moment shown in the gaussia= n
> output based on a center of mass, center of charge, or geometric cente= r for
> the origin? =A0If the last, is that based on the "Input Orientati= on" or the
> "Standard Orientation"?
>
> I did not find this info when I dove Gaussian's web pages nor a si= mple
> google search. =A0Any help would be greatly appreciated.

I got an answer to this exact question from Gaussian only last week. The dipole integrals are evaluated with whatever origin Gaussian is using
for the coordinates . These are normally the "Standard Orientation&quo= t;
coordinates and these are based on the origin at the centre of charge.
There is an IOP code to use the centre of mass.

As another poster has said, this does not affect the dipole moment, but
it defines the x, y, z axis for the cartesian components.

Brian.

> Thanks,
>
>
> Mark

--
=A0 =A0Brian Salter-Duke (Brian Duke) =A0 Brian.Salter-Duke:+:monash.edu
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Adjunct Associate Professor
=A0 =A0 =A0 =A0 =A0 =A0 Monash Institute of Pharmaceutical Sciences
=A0 =A0 =A0 Monash University Parkville Campus, VIC 3052, Australia



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--047d7b343eca00777904e58299f4-- From owner-chemistry@ccl.net Tue Sep 3 21:21:00 2013 From: "Billy McCann thebillywayne:gmail.com" To: CCL Subject: CCL:G: Transition State TS Berry Optimization Message-Id: <-49146-130903143928-3514-mhmGvCWKb97lUG8JeArnAA-x-server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary=e89a8f6433788efb3704e57f01f4 Date: Tue, 3 Sep 2013 14:39:01 -0400 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne=gmail.com] --e89a8f6433788efb3704e57f01f4 Content-Type: text/plain; charset=UTF-8 In addition to John's suggestion, I would add that calculating the force constants periodically will help towards geometric convergence, though with increased computation time. I never dug into Gaussian to find out if one could specify the number of iterations between successive force constant calculations. I just threw an 'opt=calcall' at it, which will calculate the force constants after every iteration. When finding TS's, I would typically use some sort of bond length constraint and then perform a geometry minimization. Once that is complete, I'd release the constraint. A relaxed PES scan also would help. With that, you're looking for an area where the energy is high, but the gradient is low. Also, look into the QST methods. If you're looking for a book to help you with Gaussian, you can purchase the official Gaussian book, Exploring Chemistry With Electronic Structure Methods: A Guide to Using Gaussian [1]. Also check [2] for a guide on how to use the 'opt' keyword. I keep this google operator [3] around for searching the Guassian keywords and such. Hope that helps! [1] http://amzn.com/0963676938 [2] http://www.gaussian.com/g_tech/g_ur/k_opt.htm [3] site:www.gaussian.com/g_tech/g_ur Billy Wayne McCann, Ph.D. Oak Ridge National Lab Chemical Sciences Division Chemical Separations Group On Tue, Sep 3, 2013 at 11:20 AM, Brian Jay Levandowski levandbj|a|plu.edu < owner-chemistry---ccl.net> wrote: > > Sent to CCL by: "Brian Jay Levandowski" [levandbj{}plu.edu] > Hello, > > I am running a TS Berry optimization with B3LYP 6-31+G. When the > optimization converges (after > many iterations) the output geometry is a mess.My input geometry is my > best guess from > minimizing the reactant then elongated the bond to 2.1 angstroms. I then > froze the bond at 2.1 > angstroms and did another minimization optimization to get my input > geometry for the TS search. > > In looking at the TS search intermediate gemoetries, intitially it looks > like it is headed to the TS and > possibly converging, but then it jumps to the reactant and the energy > spikes way up. It then heads > downhill and converges to a TS involving a C-C bond breaking instead of > the C-O bond I initially > elongated. > > My questions are: > 1. I took one of the intermediate geometries that looked like what I would > expect the intermediate > to look like and ran an IRC on it. It lead to the reactant and an > intermediate, but it was not a true TS > (second derivative) from the TS Berry search as it did not converge on > that geometry. So is it not the > TS I am looking for? > > 2. Could I constrain/freeze the C-C bond that is being broken in my TS > Berry optimization to > prevent the spike from happening where it enters weird geometries? Or do > constraints make the > system to artificial. > > 3. I would also like to if it is possibly to modify how much the bond > length increases and each step > in which a calculation is done. In my optimization the C-O bond starts at > 2.1 then jumps to 2.35, > 2.58, 2.83... hits 3.85 then goes back down eventually to 2.49 (this is > where I think the TS is, but it > never converges) then continues to 1.44 which is the bond length in the > reactant then is spikes and > goes askew as mentioned above. Should I try and scan the distance of the > C-O bond from say 1.85 > to around 3.0 in increments of 0.1 angstroms? If so should I also > constrain all the other variables or > does a scan constrain everything but the variables being manipulated? > > Any pointers/resources on finding TS with gaussian would also be helpful. > I am an undergrad > interested in going to grad. school for computational chemistry. I've used > Lewar's computational > chemistry but it would be great if there was a guide more specific to > gaussview/gaussian. > > Thank you, > Brian Levandowski > levandbj],[plu.edu> > > --e89a8f6433788efb3704e57f01f4 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
In addition to John's suggestion, I would add that cal= culating the force constants periodically will help towards geometric conve= rgence, though with increased computation time. =C2=A0I never dug into Gaus= sian to find out if one could specify the number of iterations between succ= essive force constant calculations. =C2=A0I just threw an 'opt=3Dcalcal= l' at it, which will calculate the force constants after every iteratio= n. =C2=A0

When finding TS's, I would typically use some sort of bo= nd length constraint and then perform a geometry minimization. =C2=A0Once t= hat is complete, I'd release the constraint. =C2=A0A relaxed PES scan a= lso would help. =C2=A0With that, you're looking for an area where the e= nergy is high, but the gradient is low. =C2=A0Also, look into the QST metho= ds. =C2=A0

If you're looking for a book to help you with Gauss= ian, you can purchase the official Gaussian book, Exploring Chemistry With = Electronic Structure Methods: A Guide to Using Gaussian [1].=C2=A0

Also check [2= ] for a guide on how to use the 'opt' keyword. =C2=A0I keep this go= ogle operator=C2=A0[3]=C2=A0around=C2=A0for searching the Guassian = keywords and such.

Hope tha= t helps! =C2=A0


Billy Wayne McCann, Ph.D.
Oak Ridge Natio= nal Lab
Chemical Sciences Division
Chemical Separations Group


On Tue,= Sep 3, 2013 at 11:20 AM, Brian Jay Levandowski levandbj|a|plu.edu <owner-chemistry---ccl.net> wrote= :

Sent to CCL by: "Brian Jay Levandowski" [levandbj{}plu.edu]
Hello,

I am running a TS Berry optimization with B3LYP 6-31+G. When the optimizati= on converges (after
many iterations) the output geometry is a mess.My input geometry is my best= guess from
minimizing the reactant then elongated the bond to 2.1 angstroms. I then fr= oze the bond at 2.1
angstroms and did another minimization optimization to get my input geometr= y for the TS search.

In looking at the TS search intermediate gemoetries, intitially it looks li= ke it is headed to the TS and
possibly converging, but then it jumps to the reactant and the energy spike= s way up. It then heads
downhill and converges to a TS involving a C-C bond breaking instead of the= C-O bond I initially
elongated.

My questions are:
1. I took one of the intermediate geometries that looked like what I would = expect the intermediate
to look like and ran an IRC on it. It lead to the reactant and an intermedi= ate, but it was not a true TS
(second derivative) from the TS Berry search as it did not converge on that= geometry. So is it not the
TS I am looking for?

2. Could I constrain/freeze the C-C bond that is being broken in my TS Berr= y optimization to
prevent the spike from happening where it enters weird geometries? Or do co= nstraints make the
system to artificial.

3. I would also like to if it is possibly to modify how much the bond lengt= h increases and each step
in which a calculation is done. In my optimization the C-O bond starts at 2= .1 then jumps to 2.35,
2.58, 2.83... hits 3.85 then goes back down eventually to 2.49 (this is whe= re I think the TS is, but it
never converges) then continues to 1.44 which is the bond length in the rea= ctant then is spikes and
goes askew as mentioned above. Should I try and scan the distance of the C-= O bond from say 1.85
to around 3.0 in increments of 0.1 angstroms? If so should I also constrain= all the other variables or
does a scan constrain everything but the variables being manipulated?

Any pointers/resources on finding TS with gaussian would also be helpful. I= am an undergrad
interested in going to grad. school for computational chemistry. I've u= sed Lewar's computational
chemistry but it would be great if there was a guide more specific to gauss= view/gaussian.

Thank you,
Brian Levandowski
levandbj],[plu.edu



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--e89a8f6433788efb3704e57f01f4-- From owner-chemistry@ccl.net Tue Sep 3 22:43:00 2013 From: "Brian J. Levandowski levandbj||plu.edu" To: CCL Subject: CCL: Transition State TS Berry Optimization Message-Id: <-49147-130903182859-28082-wwlhmYQsWxauwntyging6Q..server.ccl.net> X-Original-From: "Brian J. Levandowski " Date: Tue, 3 Sep 2013 18:28:58 -0400 Sent to CCL by: "Brian J. Levandowski " [levandbj]=[plu.edu] > "Dan Maftei dan.maftei()uaic.ro" wrote: > > Sent to CCL by: Dan Maftei [dan.maftei!=!uaic.ro] > ----_com.android.email_72308756669470 > Content-Type: text/plain; charset=utf-8 > Content-Transfer-Encoding: base64 > > RGVhciBCcmlhbiwKClRoZSBmb2xsb3dpbmcgY29uc2lkZXJhdGlvbiBtaWdodCBoZWxwOiBUUyBp > bnZvbHZlcyBub3Qgb25seSBhIGJvbmQgYnJlYWtpbmcsIGJ1dCBhbHNvIGEgbmV3IGJvbmQgdGhh > dCBpcyBmb3JtZWQgZHVyaW5nIHRoYXQgcmVhY3Rpb24gc3RlcC4gVGhlIHNhZGRsZSBwb2ludCBu > YXR1cmUgb2YgdGhlIFRTIHJlc3VsdHMgZnJvbSB0aGUgaW5jcmVhc2UvZGVjcmVhc2UgaW4gZW5l > cmd5IGNvcnJlc3BvbmRpbmcgdG8gdGhlIHR3by4gTXkgYWR2aWNlIGlzIHRvIGxvb2sgZm9yIHRo > ZSBib25kIHRoYXQgaXMgZm9ybWVkIGluIHRoZSByZWFjdGlvbiBhbmQgZnJlZXplIHRoYXQgdG9v > IChsb25nZXIgdGhhbiBpbiB0aGUgcHJvZHVjdCkgZHVyaW5nIHRoZSBwcmVsaW1pbmFyeSBvcHRp > bWl6YXRpb24uIE5leHQsIHByb2NlZWQgd2l0aCB0aGUgb3B0KFRTKSBzdGVwLgoKR29vZCBsdWNr > IQpEYW4KCiJCcmlhbiBKYXkgTGV2YW5kb3dza2kgbGV2YW5kYmp8YXxwbHUuZWR1IiA8b3duZXIt > 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