From owner-chemistry@ccl.net Tue Dec 3 02:51:01 2013 From: "Jean Jules Fifen julesfifen : gmail.com" To: CCL Subject: CCL: scaling factor in frequency calculation Message-Id: <-49397-131203022644-28140-/1DyB9xGAi07deKEs3jwxg_-_server.ccl.net> X-Original-From: Jean Jules Fifen Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 3 Dec 2013 08:26:35 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules Fifen [julesfifen#,#gmail.com] Scaling factors are better when they are applied differently in different frequencies ranges. Thus, it is okay to use dual or more scaling factors for matching experimental data. For more convenience, I can suggest you to read the paper of Robert Shields (J. Chem. Theor. Comput. 2011, 7, 2804-2817) entitled, The Role of Anharmonicity in Hydrogen-Bonded Systems: The Case of water clusters. Best regards. On 12/2/13, partha kundu partha1kundu{:}gmail.com wrote: > Dear All, > I am trying to see the effect of Cu2+ binding on a ligand by Raman > spectroscopy and trying to match those results with DFT. For the ligand, I > got a very good match with the experimental spectrum after applying a > scaling factor. However for the complex if I use the same scaling factor, I > see some modes in the 1500-1700 cm-1 regions are underestimated. If I do > not use any scaling factor in that the match is better. I am using lanl2dz > ECP and basis set combination for Cu. Is it okay to use dual scaling (0.961 > for 1000-1500 and 1 for the 1500-1700 region) for matching the experimental > data. Then I can not directly compare my theoretical results with the > experiment. Any suggestion would be of great help. > Partha > -- *-------------------------------------- * Jean Jules FIFEN, |* ** Ph. D. in Molecular Physics, |* ** Department of Physics, |* ** Faculty of Science, |* ** University of Ngaoundere, Cameroon |* ** P.O. BOX 454 Ngaoundere | * ** Phone number: 00237 75 21 61 39 | * **--------------------------------------------------------- From owner-chemistry@ccl.net Tue Dec 3 09:04:01 2013 From: "Yvonne Martin yvonnecmartin{=}gmail.com" To: CCL Subject: CCL:G: MOOCs in Computational Chemistry? Message-Id: <-49398-131203000954-21092-l0doyMzdOfd26zk6pyN12Q[A]server.ccl.net> X-Original-From: Yvonne Martin Content-Type: multipart/alternative; boundary=089e0102f83232c7d204ec9a4ed3 Date: Mon, 2 Dec 2013 23:09:47 -0600 MIME-Version: 1.0 Sent to CCL by: Yvonne Martin [yvonnecmartin,,gmail.com] --089e0102f83232c7d204ec9a4ed3 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Here is a link to a course on statistical thermo taught by Chris Cramer of the University of Minnesota: https://www.youtube.com/watch?v=3DtOEudSv6PtY I didn't see it in the current catalogue, but it could be that I searched using the wrong terms. At any rate, I heard him briefly mention the experience. In this one course he taught more students than he had previously taught in his whole career. Write him for more information. On Mon, Dec 2, 2013 at 1:18 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, Dec 02, 2013 at 11:04:17AM +0100, Alexandre Hocquet > alexandre.hocquet%x%univ-lorraine.fr wrote: > > > > Sent to CCL by: Alexandre Hocquet [alexandre.hocquet||univ-lorraine.fr] > > Dear CCLers, > > After having read this ( > http://cen.acs.org/articles/91/i12/Flipping-Chemistry-Classrooms.html) > > c&en news article about flipped classrooms (with a cameo appearence > > from one of our distinguished CCLers), i wonder if there exists such > > a thing like a "computational chemistry" MOOC, or project thereof > > that you would be aware of? > > On the one hand, computational chemistry seems to be a perfect > > candidate when it comes to doing exercices online, on the other the > > article seems to imply that MOOCs only reach a "critical mass" of > > attendees (which i suppose is mandatory for their business model) if > > they are not too "advanced" on a topic, thus excluding courses that > > are too much specialized. > > What do CCLers think? > > I think that is exactly right. I was head of a small team that started a > M. Sc. in computational chemistry that was taught entirely over the > internet way back in 1996. It attracted very few students and we closed > it in 2003 after I retired. Our web pages allowed the students to run > Gaussian, GAMESS(US) and Mopac on our servers directly from the web > page. WebMO could also be used. > > Brian. > > > -- > > *********************************************** > > Alexandre Hocquet > > > > Universit=E9 de Lorraine & Archives Henri Poincar=E9 > > Alexandre.Hocquet]~[univ-lorraine.fr > > http://poincare.univ-lorraine.fr/fr/membre-titulaire/alexandre-hocquet > > ***********************************************Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/> > > -- > 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 > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --089e0102f83232c7d204ec9a4ed3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Here is a link to a course on statistical t= hermo taught by Chris Cramer of the University of Minnesota:
https://www.youtube.com/watc= h?v=3DtOEudSv6PtY

I didn't see it in the current catalogue, but it could be tha= t I searched using the wrong terms.

At any rate, I heard him b= riefly mention the experience. In this one course he taught more students t= han he had previously taught in his whole career.

Write him for more information.


On Mon, Dec 2, 2013 at 1:18 PM, Salte= r-Duke, Brian James brian.james.duke : gmail.com <owner-chemistry]-[ccl.net> wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke]![gmail.com]
On Mon, Dec 02, 2013 at 11:04:17AM +0100, Alexandre Hocquet alexandre.hocqu= et%x%univ-lorraine.fr= wrote:
>
> Sent to CCL by: Alexandre Hocquet [alexandre.hocquet||univ-lorraine.fr]
> Dear CCLers,
> After having read this (http://cen.acs.org/ar= ticles/91/i12/Flipping-Chemistry-Classrooms.html)
> c&en news article about flipped classrooms (with a cameo appearenc= e
> from one of our distinguished CCLers), i wonder if there exists such > a thing like a "computational chemistry" MOOC, or project th= ereof
> that you would be aware of?
> On the one hand, computational chemistry seems to be a perfect
> candidate when it comes to doing exercices online, on the other the > article seems to imply that MOOCs only reach a "critical mass&quo= t; of
> attendees (which i suppose is mandatory for their business model) if > they are not too "advanced" on a topic, thus excluding cours= es that
> are too much specialized.
> What do CCLers think?

I think that is exactly right. I was head of a small team that started a M. Sc. in computational chemistry that was taught entirely over the
internet way back in 1996. It attracted very few students and we closed
it in 2003 after I retired. Our web pages allowed the students to run
Gaussian, GAMESS(US) and Mopac on our servers directly from the web
page. WebMO could also be used.

Brian.

> --
> ***********************************************
> Alexandre Hocquet
>
> Universit=E9 de Lorraine & Archives Henri Poincar=E9
> Alexandre.Hocquet]~[univ-lorraine.fr
> http://poincare.univ-lorraine.fr/fr/membre-t= itulaire/alexandre-hocquet
> ***********************************************Conferences:
> http://server.ccl.net/chemistry/announcements/conference= s/>

--
=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



-=3D This is automatically added to each message by the mailing script =3D-=
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--089e0102f83232c7d204ec9a4ed3-- From owner-chemistry@ccl.net Tue Dec 3 10:29:00 2013 From: "brupalf brupalf^umich.edu" To: CCL Subject: CCL:G: MOOCs in Computational Chemistry? Message-Id: <-49399-131203094114-17899-dYDYds+nAx6kkkCB2236Bw{}server.ccl.net> X-Original-From: brupalf Content-Type: multipart/alternative; boundary="Apple-Mail=_3E17819F-2DBA-4D0E-BFFE-A5D43399F8D4" Date: Tue, 3 Dec 2013 09:41:02 -0500 Mime-Version: 1.0 (Mac OS X Mail 6.6 \(1510\)) Sent to CCL by: brupalf [brupalf__umich.edu] --Apple-Mail=_3E17819F-2DBA-4D0E-BFFE-A5D43399F8D4 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 There's a Coursera course listed called "Biomolecular modeling on GPU", = but it's going to be in Russian: = https://www.coursera.org/course/biomodeling ciao, Bruce Bruce A. Palfey Associate Professor of Biological Chemistry & Associate Director, Program in Chemical Biology Department of Biological Chemistry University of Michigan Medical School 5220E MSRB III 1150 W. Medical Center Drive Ann Arbor, MI 48109-0606 (734) 615-2452 brupalf*umich.edu http://www.biochem.med.umich.edu/?q=3Dpalfey http://www.chembio.umich.edu/people/palfey.html http://tinyurl.com/webzyme On Dec 3, 2013, at 12:09 AM, "Yvonne Martin yvonnecmartin{=3D}gmail.com" = wrote: > Here is a link to a course on statistical thermo taught by Chris = Cramer of the University of Minnesota: > https://www.youtube.com/watch?v=3DtOEudSv6PtY >=20 > I didn't see it in the current catalogue, but it could be that I = searched using the wrong terms. >=20 > At any rate, I heard him briefly mention the experience. In this one = course he taught more students than he had previously taught in his = whole career. >=20 > Write him for more information. >=20 >=20 > On Mon, Dec 2, 2013 at 1:18 PM, Salter-Duke, Brian James = brian.james.duke : gmail.com wrote: >=20 > Sent to CCL by: "Salter-Duke, Brian James " = [brian.james.duke]![gmail.com] > On Mon, Dec 02, 2013 at 11:04:17AM +0100, Alexandre Hocquet = alexandre.hocquet%x%univ-lorraine.fr wrote: > > > > Sent to CCL by: Alexandre Hocquet = [alexandre.hocquet||univ-lorraine.fr] > > Dear CCLers, > > After having read this = (http://cen.acs.org/articles/91/i12/Flipping-Chemistry-Classrooms.html) > > c&en news article about flipped classrooms (with a cameo appearence > > from one of our distinguished CCLers), i wonder if there exists such > > a thing like a "computational chemistry" MOOC, or project thereof > > that you would be aware of? > > On the one hand, computational chemistry seems to be a perfect > > candidate when it comes to doing exercices online, on the other the > > article seems to imply that MOOCs only reach a "critical mass" of > > attendees (which i suppose is mandatory for their business model) if > > they are not too "advanced" on a topic, thus excluding courses that > > are too much specialized. > > What do CCLers think? >=20 > I think that is exactly right. I was head of a small team that started = a > M. Sc. in computational chemistry that was taught entirely over the > internet way back in 1996. It attracted very few students and we = closed > it in 2003 after I retired. Our web pages allowed the students to run > Gaussian, GAMESS(US) and Mopac on our servers directly from the web > page. WebMO could also be used. >=20 > Brian. >=20 > > -- > > *********************************************** > > Alexandre Hocquet > > > > Universit=E9 de Lorraine & Archives Henri Poincar=E9 > > Alexandre.Hocquet]~[univ-lorraine.fr > > = http://poincare.univ-lorraine.fr/fr/membre-titulaire/alexandre-hocquet > > ***********************************************Conferences: > > http://server.ccl.net/chemistry/announcements/conferences/> >=20 > -- > 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 >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- >=20 >=20 >=20 > E-mail to subscribers: CHEMISTRY- -ccl.net or use:>=20 > E-mail to administrators: CHEMISTRY-REQUEST- -ccl.net or use>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20 >=20>=20>=20 >=20 >=20 --Apple-Mail=_3E17819F-2DBA-4D0E-BFFE-A5D43399F8D4 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 https://www.coursera.= org/course/biomodeling

ciao,
Bruce<= /div>


Bruce = A. Palfey
Associate Professor of Biological Chemistry = &
Associate Director, Program in = Chemical Biology
Department of Biological = Chemistry
University of Michigan Medical School
5220E MSRB = III
1150 W. Medical Center Drive
Ann Arbor, MI 48109-0606
(734) = 615-2452
brupalf*umich.edu

http://www.= biochem.med.umich.edu/?q=3Dpalfey
http://www.chembio.umich.edu/people/p= alfey.html

On Dec 3, 2013, at 12:09 AM, "Yvonne Martin = yvonnecmartin{=3D}gmail.com" <owner-chemistry*ccl.net> = wrote:

Here is a link to a course = on statistical thermo taught by Chris Cramer of the University of = Minnesota:
https://www.youtube= .com/watch?v=3DtOEudSv6PtY

I didn't see it in the current catalogue, but it could be that = I searched using the wrong terms.

At any rate, I heard him = briefly mention the experience. In this one course he taught more = students than he had previously taught in his whole career.

Write him for more information.


On Mon, Dec 2, = 2013 at 1:18 PM, Salter-Duke, Brian James brian.james.duke : gmail.com <owner-chemistry- -ccl.net> wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke]![gmail.com]
On Mon, Dec 02, 2013 at 11:04:17AM +0100, Alexandre Hocquet = alexandre.hocquet%x%univ-lorraine.fr wrote:
>
> Sent to CCL by: Alexandre Hocquet [alexandre.hocquet||univ-lorraine.fr]
> Dear CCLers,
> After having read this (http://cen.acs.org/articles/91/i12/Flipping-Chemistry-Cl= assrooms.html)
> c&en news article about flipped classrooms (with a cameo = appearence
> from one of our distinguished CCLers), i wonder if there exists = such
> a thing like a "computational chemistry" MOOC, or project = thereof
> that you would be aware of?
> On the one hand, computational chemistry seems to be a perfect
> candidate when it comes to doing exercices online, on the other = the
> article seems to imply that MOOCs only reach a "critical mass" = of
> attendees (which i suppose is mandatory for their business model) = if
> they are not too "advanced" on a topic, thus excluding courses = that
> are too much specialized.
> What do CCLers think?

I think that is exactly right. I was head of a small team that started = a
M. Sc. in computational chemistry that was taught entirely over the
internet way back in 1996. It attracted very few students and we = closed
it in 2003 after I retired. Our web pages allowed the students to = run
Gaussian, GAMESS(US) and Mopac on our servers directly from the web
page. WebMO could also be used.

Brian.

> --
> ***********************************************
> Alexandre Hocquet
>
> Universit=E9 de Lorraine & Archives Henri Poincar=E9
> Alexandre.Hocquet]~[univ-lorraine.fr
> http://poincare.univ-lorraine.fr/fr/membre-titulaire/ale= xandre-hocquet
> ***********************************************Conferences:
> http://server.ccl.net/chemistry/announcements/conference= s/>

--
   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



-=3D This is automatically added to each message by the mailing script = =3D-



E-mail to subscribers: CHEMISTRY- = -ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST- -ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
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Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conference= s/

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

      http://www.ccl.net/spammers.txt

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



= --Apple-Mail=_3E17819F-2DBA-4D0E-BFFE-A5D43399F8D4-- From owner-chemistry@ccl.net Tue Dec 3 13:40:00 2013 From: "Rachelle Bienstock rachelleb1#,#gmail.com" To: CCL Subject: CCL: MOOCs in Computational Chemistry? Message-Id: <-49400-131203103557-17510-BDDhWlMwPqZH5LkqbGhcTw|*|server.ccl.net> X-Original-From: Rachelle Bienstock Content-Type: multipart/alternative; boundary=089e0141a4402d1ae304eca30d99 Date: Tue, 3 Dec 2013 10:35:51 -0500 MIME-Version: 1.0 Sent to CCL by: Rachelle Bienstock [rachelleb1++gmail.com] --089e0141a4402d1ae304eca30d99 Content-Type: text/plain; charset=ISO-8859-1 On the topic of MOOCs and computational chemistry... David Wild at Indiana University has posted his chemoinformatics classes and has a free online beginning chemoinformatics course http://registratio54.wix.com/learncheminformatics > He also has a link to MOOCs and other materials online relevant to chemonformatics and computational chemistry http://icep.wikispaces.com/MOOCs+and+Learning+Materials+Relevant+to+Cheminformatics Rachelle --089e0141a4402d1ae304eca30d99 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
On the topic of MOOCs and computational chemistry...<= br>
David Wild at Indiana University has posted his chemoinformatics cla= sses

and has a free online beginning=A0 chemoinformatics cours= e

http://regist= ratio54.wix.com/learncheminformatics

He = also has a link to MOOCs and other materials online relevant to chemonforma= tics and computational chemistry

Rachelle
--089e0141a4402d1ae304eca30d99--