Dear Sergio;
you= may use scf=3Dxqc option in your calculations. In many cases, it works wel= l for metallic clusters. Moreover, as noted by Reinaldo, pure functionals a= re good choice for such calculations.

best regards

Mehdi

---= ---------------------------------------------------------------------------= ------------------------------------------------

`The m= an who makes no mistakes does not usually make anything.'

= &n= bsp; = ; &n= bsp; Edward John Phelps (1822-1900)

-= ---------------------------------------------------------------------------= --------------------------------------------------
Mehdi D. Esrafili, P= h.D.

Assistant Professor of Physical Chemistry
Current = address: Department of Chemistry,

Faculty of Basic Scienc= es,University of

Maragheh, Iran.

E-mail 1: m_esrafili:_:yahoo.com
E-mail 2: esrafili:_:maragheh.ac.ir

------------------= ---------------------------------------------------------------------------= ---------------------------------

From:= Sergio Manzetti sergio.manzetti#%#gmx.com <owner-chemistry:_:ccl.net>
To: "Esrafili, Mehdi D " <m= _esrafili:_:yahoo.com>
Sent: Saturday, March 16, 2013 9:15 PM
Subject: CCL:G: Divergence in metal cluster runs

=0A

Dear all, running two cluster types= in gaussian, it is nearly impossible to reach convergence. Even though the= se are only 8 and 5 atoms, it does not converge eitehr with BLYP, MPWPW91, = PWPW91 or B3LYP.

Can it help in adding PBC? Are there other approach= es to reach convergence for difficult metal clusters?

Sergio<= /span>=0A

--406169123-1002656502-1363579266=:37585-- From owner-chemistry@ccl.net Mon Mar 18 08:53:00 2013 From: "Evgeny Blokhin jam31^^^yandex.ru" To: CCL Subject: CCL: Fundamental Question - Raman vs IR for Crystals Message-Id: <-48423-130317075755-7705-yrntrnPzbGvwmBwj34pxVA[*]server.ccl.net> X-Original-From: Evgeny Blokhin Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 17 Mar 2013 12:57:48 +0100 MIME-Version: 1.0 Sent to CCL by: Evgeny Blokhin [jam31(_)yandex.ru] Dear Vadim, thanks for the interesting question! I think, this is a kind of over-generalization, that theoretically predicted Raman spectra stay always in better agreement with experimental data than IR. In principle, my experience for perovskites does not confirm that (see e.g. dx.doi.org/10.1002/jcc.22942, dx.doi.org/10.1103/PhysRevB.83.134108). Although, some important points are to be taken into account here: the more the crystalline symmetry decreases, the more probable the BZ-centered phonon modes have both IR and Raman activity by the selection rules. Look at the Bilbao web-app to make sure: http://cryst.ehu.es/rep/sam.html Hence the calculation may predict the Raman modes and compare them with the Raman spectroscopy, however the IR spectroscopy would stay also valid. From owner-chemistry@ccl.net Mon Mar 18 09:28:00 2013 From: "Tjun Kit Min klorin2002===yahoo.co.uk" To: CCL Subject: CCL: Calculation of Magnetic Moment in Gaussian Message-Id: <-48424-130318021154-18226-apZE3PaFXvCX9o4YsABG4Q|,|server.ccl.net> X-Original-From: "Tjun Kit Min" Date: Mon, 18 Mar 2013 02:11:53 -0400 Sent to CCL by: "Tjun Kit Min" [klorin2002*yahoo.co.uk] Is the below steps are the right way to calculate Magnetic Moment in G09? 1. Get the structure with the lowest energy multiplicity. 2. Use "pop=full" to print out the "Gross Orbital Population", and then at the final (optimized) structure I sum up the "Total" column under the "Gross Orbital Population", then I divided the sum of the "Total" column by the number of atoms and I obtained the "Total Magnetic Moment per Atom". Regards Min From owner-chemistry@ccl.net Mon Mar 18 11:09:01 2013 From: "Ambrish K Srivastava ambrishphysics!A!gmail.com" To: CCL Subject: CCL: Calculation of Magnetic Moment in Gaussian Message-Id: <-48425-130318110648-17593-7/BvtmUMduWwQW4IAfxbQg-,-server.ccl.net> X-Original-From: Ambrish K Srivastava Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 18 Mar 2013 20:36:37 +0530 MIME-Version: 1.0 Sent to CCL by: Ambrish K Srivastava [ambrishphysics-$-gmail.com] Dear all, I want to add something further in this query- How to calculate particular orbital contribution to total magnetic moment ? Hope to see you helpful suggestions.. On 3/18/13, Tjun Kit Min klorin2002===yahoo.co.uk wrote: > > Sent to CCL by: "Tjun Kit Min" [klorin2002*yahoo.co.uk] > Is the below steps are the right way to calculate Magnetic Moment in G09? > > 1. Get the structure with the lowest energy multiplicity. > > 2. Use "pop=full" to print out the "Gross Orbital Population", and then at > the final (optimized) structure I sum up the "Total" column under the "Gross > Orbital Population", then I divided the sum of the "Total" column by the > number of atoms and I obtained the "Total Magnetic Moment per Atom". > > Regards > Min> > > -- *Ambrish K. Srivastava CSIR Junior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007* From owner-chemistry@ccl.net Mon Mar 18 11:43:00 2013 From: "James Gary Prudhomme jprudhomme]_[healthtech.com" To: CCL Subject: CCL: Structure-Based Drug Design for Epigenetic Targets Course Message-Id: <-48426-130318102752-7550-CIPC/td8Nz8o3G2FJlW0IA%a%server.ccl.net> X-Original-From: "James Gary Prudhomme" Date: Mon, 18 Mar 2013 10:27:51 -0400 Sent to CCL by: "James Gary Prudhomme" [jprudhomme:healthtech.com] When: June 19, 2013 (9:00 am - 12:00 pm) Where: The Revere Hotel, Boston, MA Epigenetic processes are the focus of intense interest, and the families of proteins that mediate epigenetic signalling are a highly promising source of new drug targets. Tackling this emerging field of novel drug targets is not without its challenges. This workshop will review the contribution that structural biology has made to the discovery of small molecule modulators. Structural information can be invaluable in determining the druggability of potential targets, and in enabling more efficient identification of hit molecules. Structural information can also guide the design of compounds with improved affinity for the target, or selectivity versus other targets. This introductory course on drug design for epigenetic targets will focus especially on emerging targets such as bromodomain (readers), methyltransferase (writers) and lysine demethylase (erasers). Instructors: Johnathan R. Whetstine, Ph.D., Assistant Professor of Medicine, Harvard Medical School Philip Fallon, Ph.D., Senior Medicinal Chemist, Domainex Ltd. This short course will take place prior to the start of CHI's Structure-Based Drug Design Conference (http://www.healthtech.com/sbd) Go to our website to register and view full details on this short course and the SBDD conference. From owner-chemistry@ccl.net Mon Mar 18 12:18:01 2013 From: "Andras Borosy andras.borosy()givaudan.com" To: CCL Subject: CCL: Visualisation of molecular networks Message-Id: <-48427-130318120144-15934-Leig7+kJMImE33FdM0VFwg]~[server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 0057FC14C1257B32_=" Date: Mon, 18 Mar 2013 17:01:32 +0100 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy{:}givaudan.com] This is a multipart message in MIME format. --=_alternative 0057FC14C1257B32_= Content-Type: text/plain; charset="US-ASCII" Dear Colleagues, I would need a commercial application to display molecular networks (like http://www.cytoscape.org/ but with a decent technical support). Might you suggest me some? Many thanks, Andras Borosy --=_alternative 0057FC14C1257B32_= Content-Type: text/html; charset="US-ASCII" Dear Colleagues,

I would need a commercial application to display molecular networks (like http://www.cytoscape.org/ but with a decent technical support).

Might you suggest me some?

Many thanks,

Andras Borosy --=_alternative 0057FC14C1257B32_=-- From owner-chemistry@ccl.net Mon Mar 18 16:47:00 2013 From: "Marc Baaden baaden%smplinux.de" To: CCL Subject: CCL: Visualisation of molecular networks Message-Id: <-48428-130318144731-5700-o2iJABfsNRDBbDLSS8DDqQ-x-server.ccl.net> X-Original-From: Marc Baaden Content-Type: text/plain; charset=us-ascii Date: Mon, 18 Mar 2013 19:49:39 +0100 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden]^[smplinux.de] Dear Andras, I am not sure I understand in what sense you mean commercial application, but if it's of any interest, our recently released UnityMol molecular viewer can read and visualize Cytoscape format in original ways (among other things). Technical support might be a bit more limited :) Please do see for yourself an example image of a network in toon rendering: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057990.g006/largerimage The software (Mac, Win, Linux, Source) can be obtained from http://unitymol.sourceforge.net and is described in more detail here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0057990 (Title: Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges) Best, Marc owner-chemistry a ccl.net said: >>Dear Colleagues, >>I would need a commercial application to display molecular networks >>(like http://www.cytoscape.org/ but with a decent technical support). >>Might you suggest me some? >>Many thanks, >>Andras Borosy -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden a smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From owner-chemistry@ccl.net Mon Mar 18 18:16:01 2013 From: "Arthur Zalevsky aozalevsky::gmail.com" To: CCL Subject: CCL: Visualisation of molecular networks Message-Id: <-48429-130318181423-15018-aWrnx/gsYWYGuGjGFRmmFQ+/-server.ccl.net> X-Original-From: Arthur Zalevsky Content-Type: text/plain; charset=UTF-8 Date: Tue, 19 Mar 2013 02:14:16 +0400 MIME-Version: 1.0 Sent to CCL by: Arthur Zalevsky [aozalevsky+*+gmail.com] Try to look at yEd: http://www.yworks.com/en/products_yed_about.html Cytoscape has GraphML export plugin and yEd works well with it. There are a couple of examples in gallery, already, which shows it's capabilities in the same task. http://www.yworks.com/en/products_yed_gallery.html yEd also has optional commercial support http://www.yworks.com/en/services.html Regards, Arthur Zalevsky 2013/3/18 Andras Borosy andras.borosy()givaudan.com : > Dear Colleagues, > > I would need a commercial application to display molecular networks (like > http://www.cytoscape.org/ but with a decent technical support). > > Might you suggest me some? > > Many thanks, > > Andras Borosy From owner-chemistry@ccl.net Mon Mar 18 20:27:00 2013 From: "Avinash raju avi0raju|a|gmail.com" To: CCL Subject: CCL:G: Regarding software for viewing gaussian output Message-Id: <-48430-130318194616-17371-E9OM7LeUwjWzo8ZqEhpuSg(_)server.ccl.net> X-Original-From: "Avinash raju" Date: Mon, 18 Mar 2013 19:46:15 -0400 Sent to CCL by: "Avinash raju" [avi0raju,+,gmail.com] hi i need a software which i can use to open the gaussian output files and draw different kind of structures of the molecules such as ball and stick model and wireframe models and also what would be the best method to get bond length and angles indicated or written on the molecules structure. thank you avinash From owner-chemistry@ccl.net Mon Mar 18 23:20:00 2013 From: "John Keller jwkeller-*-alaska.edu" To: CCL Subject: CCL:G: Regarding software for viewing gaussian output Message-Id: <-48431-130318231809-30781-/pAqj0OeN2Hs7HRN0RTN7w-,-server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=14dae94ee2adadddc404d83e8d7f Date: Mon, 18 Mar 2013 19:18:03 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller!^!alaska.edu] --14dae94ee2adadddc404d83e8d7f Content-Type: text/plain; charset=ISO-8859-1 Hi Avinash, You didn't say what your operating system is, but here are a few programs I am aware of that are free and can process, in various ways, Gaussian output. I'll bet there are at least a dozen more that will be mentioned by others. Molekel is the one I would start with. molekel multiwfn webmo vmd jmol gOpenMol Molden Avogadro Jamberoo Best Regards, John Keller On Mon, Mar 18, 2013 at 3:46 PM, Avinash raju avi0raju|a|gmail.com < owner-chemistry-.-ccl.net> wrote: > > Sent to CCL by: "Avinash raju" [avi0raju,+,gmail.com] > hi > > i need a software which i can use to open the gaussian output files and > draw different kind of structures of the molecules such as ball and stick > model and wireframe models and also what would be the best method to get > bond length and angles indicated or written on the molecules structure. > > thank you > > avinash> > > --14dae94ee2adadddc404d83e8d7f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi Avinash,
You didn't say what your oper= ating system is, but here are a few programs I am aware of that are free an= d can process, in various ways, Gaussian output. I'll bet there are at = least a dozen more that will be mentioned by others. Molekel is the one I w= ould start with.
molekel
multiwfn
webmo
vmd
jmol
gOpenMol
Molden
Avogad= ro
Jamberoo

Best Regards,

John Keller

On Mon, Mar = 18, 2013 at 3:46 PM, Avinash raju avi0raju|a|g= mail.com <owner-chemistry-.-ccl.net> wrote:

Sent to CCL by: "Avinash =A0raju" [avi0raju,+,gmail.com]
hi

i need a software which i can use to open the gaussian output files and dra= w different kind of structures of the molecules such as ball and stick mode= l and wireframe models and also what would be the best method to get bond l= ength and angles indicated or written on the molecules structure.

thank you

avinash

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