From owner-chemistry@ccl.net Fri Jun 9 04:25:00 2017 From: "Benoit BRAIDA benoit.braida:-:upmc.fr" To: CCL Subject: CCL: Chemical Bonding conference CB2017 -- Second circular Message-Id: <-52831-170609042345-30099-ukQpUWh4NMINEZZ0xH+NTA*server.ccl.net> X-Original-From: "Benoit BRAIDA" Date: Fri, 9 Jun 2017 04:23:43 -0400 Sent to CCL by: "Benoit BRAIDA" [benoit.braida^^^upmc.fr] Dear Colleagues, The conference "The Chemical Bonds at the 21st Century - 2017" will takes place in Aachen (Germany) next September 2-4, as a 2017 WATOC official satellite. We are getting close of these important deadlines: ===> Early bird inscription fees: until June 15. ===> Deadline for abstract submission (oral talk or poster): July 1 Please note that there is a significant number of slots for oral talks that are open upon selection (young researchers will be favored in particular). A tutorial on Valence Bond theory and the XMVB program will also takes places right after the conference (Sept 4-7). http://cb2017.rwth-aachen.de/CB2017-registration.html The organizers, Arne Lchow and Benot Brada From owner-chemistry@ccl.net Fri Jun 9 09:53:00 2017 From: "Ulrike Salzner salzner*_*fen.bilkent.edu.tr" To: CCL Subject: CCL: symmetry breaking Message-Id: <-52832-170609085932-23714-hM0A5thQV7mCOX3UXEbo3Q*o*server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: multipart/alternative; boundary="94eb2c0877fcffbed80551868906" Date: Fri, 9 Jun 2017 15:59:25 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner###fen.bilkent.edu.tr] --94eb2c0877fcffbed80551868906 Content-Type: text/plain; charset="UTF-8" Hello, I am comparing three large conjugated pi-systems with density functional theory (global and range-separated hybrids). The difference between them is that one contains phenyl rings, one thiophene, and the last one selenophene. All three of molecules have UDFT instability with B3P86 with 30% HF exchange. With open-shell singlet calculations and 50:50 HOMO-LUMO mixing, the phenyl and seleophene systems converge to open-shell biradical ground states that lie 0.02 and 0.12 eV below the closed-shell states. The thiophene system does not break the symmetry. This is odd because selenophene and thiophene system behave usually very similar. In addition, excited calculations with UTDDFT give negative triplet excitation energies for all of them when the closed-shell wave are used. As triplet excitation energies are probably underestimated with UTDDFT, I checked the ground state triplet energies. The triplets lie 1.24 eV (phen), 0.79 eV (thio), and 0.61 eV (seleno) above the closed-shell singlets. Again there is no reason why the thiophene system should differ > from the other two. Is there any way other way to find the broken the symmetry ground state? Or - is the lack of a broken symmetry solution after 50:50 HOMO-LUMO mixing sufficient to prove that the ground state is closed-shell? Thanks for suggestions, Ulrike -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara --94eb2c0877fcffbed80551868906 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello,
I am comparing three large conju= gated pi-systems with density functional theory (global and range-separated= hybrids). The difference between them is that one contains phenyl rings, o= ne thiophene, and the last one selenophene.=C2=A0

All three of mole= cules have UDFT instability with B3P86 with 30% HF exchange.

With o= pen-shell singlet calculations and 50:50 HOMO-LUMO mixing, the phenyl and s= eleophene systems converge to open-shell biradical ground states that lie = 0.02 and 0.12 eV below the closed-shell states. The thiophene system does n= ot break the symmetry. This is odd because selenophene and thiophene system= behave usually very similar.

In addition, excited calcu= lations with UTDDFT give negative triplet excitation energies for all of th= em when the closed-shell wave are used.

As triplet excitation energi= es are probably underestimated with UTDDFT, I checked the ground state trip= let energies.=C2=A0 The triplets lie 1.24 eV (phen), 0.79 eV (thio), and 0.= 61 eV (seleno) above the closed-shell singlets. Again there is no reason wh= y the thiophene system should differ from the other two.

= Is there any way other way to find the broken the symmetry ground state? Or - is the lack o= f a broken symmetry solution after 50:50 HOMO-LUMO mixing sufficient to pro= ve that the ground state is closed-shell?

Thanks for sugg= estions,
Ulrike
--
Assoc. Prof. Ulrike Salzner
Department of Chemistry
Bilkent Un= iversity
06800 Bilkent, Ankara
--94eb2c0877fcffbed80551868906-- From owner-chemistry@ccl.net Fri Jun 9 11:55:01 2017 From: "Mark Mackey mark~!~cresset-group.com" To: CCL Subject: CCL:G: Educational software for molecular modeling/computational chemistry co Message-Id: <-52833-170609114421-27599-VhHFY1DZjbVXN/y0zzwM2A%server.ccl.net> X-Original-From: Mark Mackey Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 9 Jun 2017 15:44:13 +0000 MIME-Version: 1.0 Sent to CCL by: Mark Mackey [mark]=[cresset-group.com] Cresset’s policy is to make our software freely available for teaching purposes where possible. While we don’t currently provide a QM solution, our software products cover most of the other applications mentioned by Prof. Major (ligand alignment, protein modelling, pharmacophores, docking, QSAR etc), and we also provide a range of training material that could be very useful for anyone setting up or running a computational course. We endeavour to make the user interface as simple as possible, so the learning curve for the students should be low. You can get details on the teaching licenses (and on the rest of our academic licensing program and bursary program providing free software for students) at http://www.cresset-group.com/academic-licensing Regards, Mark -- Mark Mackey Chief Scientific Officer Cresset New Cambridge House, Bassingbourn Road, Litlington, Cambridgeshire, SG8 0SS, UK tel: +44 (0)1223 858890    mobile: +44 (0)7595 099165    fax: +44 (0)1223 853667 email: mailto:mark() cresset-group.com    web: http://www.cresset-group.com/    skype: mark_cresset > From: owner-chemistry+mark==cresset-bmd.com() ccl.net [mailto:owner-chemistry+mark==cresset-bmd.com() ccl.net] On Behalf Of Joe Leonard jleonard42__gmail.com Sent: 08 June 2017 14:32 To: Mark Mackey Subject: CCL:G: Educational software for molecular modeling/computational chemistry co Have you considered Spartan?  It has been successfully used in both educational and commercial work for deades and (I think) covers many of the areas you describe.  It also has a tablet application that might be useful as a replacement for the tinker-toy models used “when I was a boy”. It’s possible one of the commercial vendors (Schrodinger, OpenEye, CCG) might work with academic sites that offer training on a recurring basis as it is a marketing effort for them.  I have no idea whether this is still done (Accelrys was known for this if I remember correctly).  Perhaps you should contact their Academic Sales contacts to see whether a workshop or an on-going relationship can be set up? Joe On Jun 8, 2017, at 8:07 AM, Dan T Major majort^^^http://biu.ac.il wrote: Sent to CCL by: "Dan T Major" [majort()http://biu.ac.il] Dear Colleagues, I would like your advice regarding educational software for molecular modeling/computational chemistry courses. In my department, we have been giving a course in molecular modeling for some years now that includes lectures and hands-on sessions. Its a rather extensive course that covers potential energy surfaces (molecular mechanics, quantum chemistry), minimization methods, molecular dynamics, solvation, docking, protein modeling, pharmacophores, and some solid-state modeling using DFT. The course has been geared towards a general graduate student audience (not specialists) to expose young researchers to modeling. The course includes a final project related to their area of research. The hands-on part of the course is an essential part of the course and we have used Discovery Studio and Materials Studio (Biovia). Due to continuously increasing costs it has now become too expensive for us, and we are looking for much cheaper alternatives that have similar easy intuitive GUI for a wide range of applications (to minimize the need for students to spend time learning many different programs). We have many existing platforms, but none really fill this need (i.e. Gaussian, Q-Chem, CHARMM, Amber, VASP, Autodock, etc.). Schrodinger is currently also on the expensive side for educational purposes. Any ideas? Thank you, Prof. Dan T Major Chemistry Department Bar-Ilan University Ramat-Gan 52900 Israel Phone: 972-3-5317392 Fax: 972-3-7384053 e-mail:majort]~[http://mail.biu.ac.il(majort]~[biu.ac.ilorDan-Thomas.Major]~[http://biu.ac.il) Web:http://ch.biu.ac.il/major --> New Web-site:https://faculty.biu.ac.il/~majord -->GoogleScholar(https://scholar.google.co.il) -->ResearchID(http://www.researcherid.com/rid/J-8761-2014) -->ORCID(http://orcid.org/0000-0002-9231-0676) -->ResearchGate(https://www.researchgate.net/profile/Dan_Major)the strange characters on the top line to the *_* sign. You can alsoE-mail to subscribers: mailto:CHEMISTRY*_*ccl.net or use:      http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: mailto:CHEMISTRY-REQUEST*_*ccl.net or use      http://www.ccl.net/cgi-bin/ccl/send_ccl_message      http://www.ccl.net/chemistry/sub_unsub.shtml     http://www.ccl.net/spammers.txt— “We’re all told at some point that we can no longer play the children’s game.  We just don’t know when that’s gonna be.  Some of us are told at 18, some of are told at 40, but we’re all told.”   — Moneyball From owner-chemistry@ccl.net Fri Jun 9 13:51:00 2017 From: "Billy McCann thebillywayne ~ gmail.com" To: CCL Subject: CCL: MM3 parameters Message-Id: <-52834-170609134704-8852-SeJ9tFt3NUkDlIwi70iy1Q[#]server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary="001a1140ec6858e9cd05518a8e3c" Date: Fri, 9 Jun 2017 13:46:43 -0400 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne]|[gmail.com] --001a1140ec6858e9cd05518a8e3c Content-Type: text/plain; charset="UTF-8" Hi Nick. Check Benjamin Hay's papers. He's done a lot of work extending MM3 over the years and parameters are always given in the Supp Info. Here's his linkedin https://www.linkedin.com/in/benjaminhay/ Hope that helps. -- Billy Wayne McCann, Ph.D. "There is nothing new under the sun." ~ The Preacher --001a1140ec6858e9cd05518a8e3c Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi Nick.

Check Benjamin Hay's papers. He's = done a lot of work extending MM3 over the years and parameters are always g= iven in the Supp Info. Here's his linkedin https://www.linkedin.com/in/benjaminhay/
<= br>Hope that helps.

--
Billy Wayne McCann, Ph.D.
"There = is nothing new under the sun." ~ The Preacher
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