From owner-chemistry@ccl.net Fri Jun 17 07:41:00 2011 From: "Gustavo Mercier gamercier ~~ yahoo.com" To: CCL Subject: CCL: Algorithm for the point group determination of arbitrary molecules Message-Id: <-44918-110617062742-18789-3QStjJbQOz83MthAqNW8yg^server.ccl.net> X-Original-From: Gustavo Mercier Content-Type: multipart/alternative; boundary="0-677089790-1308306449=:67836" Date: Fri, 17 Jun 2011 03:27:29 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Gustavo Mercier [gamercier.:.yahoo.com] --0-677089790-1308306449=:67836 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi!=0A=0AYou may want to look into this paper...=0A=0AZabrodsky et al. (199= 3) JACS, 115, 8278-8298=0A=0AIt describes a continuous symmetry metric to m= easure deviations from idealized point groups.=0A=0AA while back Tullio Pil= ati and Alessandra Forni developed a program they called Symmol to "symmetr= ize" coordinates. I believe the program may be in the ccl archives. If=A0 r= emember correctly, the program required the input of a tolerance to the dev= iation from an idealized point group, but did not require defining the poin= t group to which you would 'symmetrize'. This makes me believe that the pro= gram had an algorithm to define the 'closest' point group that you may use = in your work.=0A=0ALook at the following reference:=0A=0APilati, T. & Forni= , A. (1998). J. Appl. Cryst. 31 , 503-504=0A=0AGood luck.=0A=0A=A0=0A=0A--= =0AGustavo A. Mercier, Jr., MD, PhD=0Agamercier/./yahoo.com=0AGustavo.Mercier= /./bmc.org=0Agumercie/./bu.edu=0A617-414-6440=0A=0A=0A=0A=0A>__________________= ______________=0A>From: Srikanth Patala srikanth.patala ~~ gmail.com =0A>To: "Mercier, Gustavo, " =0A>Sent: Thursday, June 16, 2011 4:00 PM=0A>Subject: CCL: Algorithm for = the point group determination of arbitrary molecules=0A>=0A>Dear Michel,=0A= >=0A>Thank you very much for your response and the link to the freeware. I = also realized that my question is slightly misleading. I do not yet have a = working code for determination of point group symmetries of arbitrary molec= ules (symmetric without deviations). I am still working on it and I jumped = a couple of steps ahead and posted a question about deviation from symmetri= es (which is also something that I absolutely require). I am basically tryi= ng to calculate the moment of inertia tensor to determine the point groups = but I am not aware of a good (efficient) algorithm to determine point symme= tries for static, symmetric molecules. Any help with this first step is als= o greatly appreciated.=0A>=0A>Thanks,=0A>Srikanth=0A>=0A>=0A>On Thu, Jun 16= , 2011 at 12:13 PM, Michel Petitjean petitjean.chiral]~[gmail.com wrote:=0A>=0A>=0A>>Sent to CCL by: Michel Petitjean [petit= jean.chiral!=3D!gmail.com]=0A>>Dear Srikanth,=0A>>Such a code would work un= der the assumption that the symmetry is not=0A>>too much distorted.=0A>>You= may check the deviation from direct symmetry with the direct=0A>>symmetry = index (DSI) and the deviation from achirality with the chiral=0A>>index (CH= I), both computable with the QCM freeware:=0A>>http://petitjeanmichel.free.= fr/itoweb.petitjean.freeware.html=0A>>Best regards,=0A>>Michel.=0A>>=0A>>Mi= chel Petitjean=0A>>MTi, INSERM UMR-S 973, University Paris 7=0A>>35 rue Hel= ene Brion, 75205 Paris Cedex 13, France.=0A>>Phone: +331 5727 8434; Fax: +3= 31 5727 8372=0A>>E-mail: petitjean.chiral=3D-=3Dgmail.com (preferred),=0A>>= michel.petitjean=3D-=3Duniv-paris-diderot.fr=0A>>http://petitjeanmichel.fre= e.fr/itoweb.petitjean.html=0A>>=0A>>=0A>>2011/6/16 Srikanth Patala srikanth= .patala ~~ gmail.com=0A>>:=0A>>=0A>>>=0A>>> = Sent to CCL by: "Srikanth =A0Patala" [srikanth.patala-*-gmail.com]=0A>>> He= llo all,=0A>>>=0A>>> I am trying to write a code to determine the point gro= up of arbitrary shapes (clusters of atoms). I am very well aware of all the= point symmetries and I did find some suggestions online (flowcharts) for d= eveloping such a code. The main problem now is that I have temperature in m= y system and hence the shape of the clusters fluctuates. I am not sure how = to have a code while allowing for deviation from symmetric structure. There= is an applet online that allows for this deviation: http://www.colby.edu/c= hemistry/PChem/scripts/ABC.html=0A>>>=0A>>> I would like to perform the exa= ct same calculations using a code. Any suggestions?? Thanks in advance for = your time.=0A>>>=0A>>> Thanks,=0A>>> Srikanth=0A>>>=0A>>=0A>>=0A>>=0A>>-=3D= This is automatically added to each message by the mailing script =3D-=0A>= >=0A>>E-mail to subscribers: CHEMISTRY*ccl.net or use:=0A>>=A0 =A0 =A0http:= //www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>>=0A>>E-mail to administrator= s: CHEMISTRY-REQUEST*ccl.net or use=0A>>=A0 =A0 =A0http://www.ccl.net/cgi-b= in/ccl/send_ccl_message=0A>>=0A>>Subscribe/Unsubscribe:=0A>>=A0 =A0 =A0http= ://www.ccl.net/chemistry/sub_unsub.shtml=0A>>=0A>>Before posting, check wai= t time at: http://www.ccl.net=0A>>=0A>>Job: http://www.ccl.net/jobs=0A>>Con= ferences: http://server.ccl.net/chemistry/announcements/conferences/=0A>>= =0A=0A= >>=0A>>=A0 =A0 =A0http://www.ccl.net/spammers.txt=0A>>=0A>>RTFI: http://www= .ccl.net/chemistry/aboutccl/instructions/=0A>>=0A>>=0A>>=0A>=0A>=0A>-- =0A>= Srikanth=0A>=0A>=0A> --0-677089790-1308306449=:67836 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi!
=
You may want to look into this paper...

Zabrodsky et al. (1993) J= ACS, 115, 8278-8298

It d= escribes a continuous symmetry metric to measure deviations from idealized = point groups.

A while ba= ck Tullio Pilati and Alessandra Forni developed a program they called Symmo= l to "symmetrize" coordinates. I believe the program may be in the ccl arch= ives. If  remember correctly, the program required the input of a tole= rance to the deviation from an idealized point group, but did not require d= efining the point group to which you would 'symmetrize'. This makes me beli= eve that the program had an algorithm to define the 'closest' point group that you may use in your work.

Look at the following reference:

<= /span>
Pilati, T. & Forni, A. (1998). = J. Appl. Cryst. = 31 , 503-504=

Good luck.
=  

--
Gustavo A. Mercier, Jr., MD, PhD
gamercier/./ya= hoo.com
Gustavo.Mercier/./bmc.org
gumercie/./bu.edu
617-414-6440

<= hr size=3D"1">From: Srikant= h Patala srikanth.patala ~~ gmail.com <owner-chemistry/./ccl.net>
To: "Mercier, Gustavo, " <= ;gamercier/./yahoo.com>
Sent: Thursday, June 16, 2011 4:00 PM
Subject: CCL: Algorithm for the point group determination = of arbitrary molecules

=0ADear Michel,

Thank you very = much for your response and the link to the freeware. I also realized that m= y question is slightly misleading. I do not yet have a working code for det= ermination of point group symmetries of arbitrary molecules (symmetric with= out deviations). I am still working on it and I jumped a couple of steps ah= ead and posted a question about deviation from symmetries (which is also so= mething that I absolutely require). I am basically trying to calculate the = moment of inertia tensor to determine the point groups but I am not aware o= f a good (efficient) algorithm to determine point symmetries for static, sy= mmetric molecules. Any help with this first step is also greatly appreciate= d.
=0A=0A
Thanks,
Srikanth

On Thu, Jun 16, 2011 at 12:13 PM, Michel Petitjean petitjean.chiral= ]~[gmail.co= m <o= wner-chemistry*ccl.net> wrote:
=0A=0A

=0ASent to CCL by: Michel Petitjean [petitjean.= chiral!=3D!= gmail.com]
=0ADear Srikanth,
=0ASuch a code would work under the = assumption that the symmetry is not
=0Atoo much distorted.
=0AYou may= check the deviation from direct symmetry with the direct
=0Asymmetry in= dex (DSI) and the deviation from achirality with the chiral
=0Aindex (CH= I), both computable with the QCM freeware:
=0Ahttp://petitjeanmichel.fre= e.fr/itoweb.petitjean.freeware.html
=0ABest regards,
=0AMichel.
= =0A
=0AMichel Petitjean
=0AMTi, INSERM UMR-S 973, University Paris 7<= br>=0A35 rue Helene Brion, 75205 Paris Cedex 13, France.
=0APhone: +331 5727 8434; Fax: +331 5727 8372<= /a>
=0AE-mail: petitjean.chiral=3D-=3Dgmail.com (preferred),
=0Amichel.petit= jean=3D-=3Duniv-paris-diderot.fr
=0Ahttp://petitjeanmichel.free.fr/= itoweb.petitjean.html
=0A
=0A
=0A2011/6/16 Srikanth Patala srikant= h.patala ~~ gmail.com
=0A<owner-chemistry=3D-=3Dccl.net>:
=0A
=
>
=0A> Sent to CCL by: "Srikanth &n= bsp;Patala" [srikanth.patala-*-gmail.com]
=0A> Hello all,
=0A>
= =0A> I am trying to write a code to determine the point group of arbitra= ry shapes (clusters of atoms). I am very well aware of all the point symmet= ries and I did find some suggestions online (flowcharts) for developing suc= h a code. The main problem now is that I have temperature in my system and = hence the shape of the clusters fluctuates. I am not sure how to have a cod= e while allowing for deviation from symmetric structure. There is an applet= online that allows for this deviation: http://www.colby.edu/chemistry/PChe= m/scripts/ABC.html
=0A=0A=0A>
=0A> I would like to perform the = exact same calculations using a code. Any suggestions?? Thanks in advance f= or your time.
=0A>
=0A> Thanks,
=0A> Srikanth
=0A><= br>=0A
=0A
=0A
=0A-=3D This is automatically added to each message= by the mailing script =3D-
=0A
=0AE-mail to subscribers: CHEMISTRY*ccl.net or use:
=0A     &= nbsp;http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=0A
=0AE-mail to= administrators: CHEMISTR= Y-REQUEST*ccl.net or use
=0A      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=0A
=0ASubscribe= /Unsubscribe:
=0A      http://www.ccl.net/chemistry/sub_u= nsub.shtml
=0A
=0ABefore posting, check wait time at: http://www.ccl.= net
=0A
=0AJob: http://www.ccl.net/jobs
=0AConferences: http://ser= ver.ccl.net/chemistry/announcements/conferences/
=0A
=0ASearch Messag= es: http://www.ccl.net/chemistry/searchccl/index.shtml
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=0A
=0ARTFI: http://www= .ccl.net/chemistry/aboutccl/instructions/
=0A
=0A
=0A
<= /blockquote>



--
Srikanth


--0-677089790-1308306449=:67836-- From owner-chemistry@ccl.net Fri Jun 17 08:15:01 2011 From: "Jens Spanget-Larsen spanget.%%.ruc.dk" To: CCL Subject: CCL: Weaknesses of the INDO/S method Message-Id: <-44919-110617050811-7601-ALyIErVk+R1PnUcRnOFAgw%%server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Type: multipart/alternative; boundary="------------020604020705020502050601" Date: Fri, 17 Jun 2011 11:07:57 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget]|[ruc.dk] This is a multi-part message in MIME format. --------------020604020705020502050601 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear Gustavo, for what it is worth: One weakness of INDO/S and other NDO methods is failure to predict the so-called pairing properties for the pi-systems of alternant hydrocarbons, see for example Theoret. Chem. Acc. 98, 137-153 (1997). Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget!A!ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ On 6/16/2011 19:30, Gustavo L.C. Moura gustavo.moura^ufpe.br wrote: > Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura,,ufpe.br] > Dear CCL Readers, > I am looking for a reference that discusses the strong points and the weaknesses of the semiempirical INDO/S method for calculating electronic spectra. Where does the method work really well? Where does the method perform poorly? I need such reference to add to a manuscript I am writing right now. Any pointers are welcome. > Thank you very much in advance. > Sincerely yours, > Gustavo L.C. Moura> > --------------020604020705020502050601 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Dear Gustavo,
for what it is worth: One weakness of INDO/S and other NDO methods is failure to predict the so-called pairing properties for the pi-systems of alternant hydrocarbons, see for example Theoret. Chem. Acc. 98, 137-153 (1997).
Jens >--<
 
  ------------------------------------------------------
  JENS SPANGET-LARSEN         Office:      +45 4674 2710
  Dept. of Science (18.1)     Fax:         +45 4674 3011
  Roskilde University         Mobile:      +45 2320 6246
  P.O.Box 260                 E-Mail:     spanget!A!ruc.dk
  DK-4000 Roskilde, Denmark   http://www.ruc.dk/~spanget
  ------------------------------------------------------

On 6/16/2011 19:30, Gustavo L.C. Moura gustavo.moura^ufpe.br wrote: 
Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura,,ufpe.br]
Dear CCL Readers,
	I am looking for a reference that discusses the strong points and the weaknesses of the semiempirical INDO/S method for calculating electronic spectra. Where does the method work really well? Where does the method perform poorly? I need such reference to add to a manuscript I am writing right now. Any pointers are welcome.
	Thank you very much in advance.
	Sincerely yours,
			Gustavo L.C. MouraE-mail to subscribers: CHEMISTRY!A!ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net or use
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RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
--------------020604020705020502050601-- From owner-chemistry@ccl.net Fri Jun 17 08:51:01 2011 From: "Serdar Badoglu sbadoglu{}gazi.edu.tr" To: CCL Subject: CCL: band deconvolution Message-Id: <-44920-110617062608-14885-ELjJR76Jei49Qp0WTL0ytw%server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Fri, 17 Jun 2011 06:26:06 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu]|[gazi.edu.tr] Hi CCL'ers I need to learn about the basics of band deconvolution analysis (for IR). Also, I'm looking for a software (preferably free for academic use) which can carry out BDA calculations. Any suggestions? Regards. From owner-chemistry@ccl.net Fri Jun 17 10:49:00 2011 From: "Andrea Lombardi ebiu2005|-|gmail.com" To: CCL Subject: CCL: J. C. Rayez THEOCHEM Special Issue Message-Id: <-44921-110617104643-16858-28jAhrJ5nLTlKcgrUUhRcQ**server.ccl.net> X-Original-From: "Andrea Lombardi" Date: Fri, 17 Jun 2011 10:46:41 -0400 Sent to CCL by: "Andrea Lombardi" [ebiu2005_._gmail.com] Dear Colleagues, It was our pleasure to announce a few months ago that we are organizing the publication of a special issue in honor of Prof. Jean-Claude Rayez's achievements in the journal "Computational and Theoretical Chemistry" (formerly known as: Journal of Molecular Structure: THEOCHEM). The overall theme is "Chemical reactivity: from accurate theories to simple models". It is thus broad enough for researchers in molecular dynamics or electronic structure of small to large systems, within gas or condensed phases, to be able to contribute. Elsevier plans to set up Elsevier Editorial System (EES) in June for authors' submission. The deadline for submitting manuscripts is end of September. Contributors are refered to the author guide at http://www.elsevier.com/wps/find/journaldescription.cws_home/724323/authorinstructions They will have to upload their papers by selecting "Rayez Issue on Reactivity" in the drop down menu in EES submission page in June. Best regards, The Guest Editors, Laurent Bonnet, Bordeaux University/CNRS, France Email : l.bonnet\a/ism.u-bordeaux1.fr Pascal Larregaray, Bordeaux University/CNRS, France Email : p.larregaray\a/ism.u-bordeaux1.fr Vincenzo Aquilanti, University of Perugia, Italy Email : aquila\a/dyn.unipg.it, vincenzoaquilanti\a/yahoo.it To join or leave the molecular-dynamics-news email list, go to: http://www.jiscmail.ac.uk/lists/molecular-dynamics-news.html From owner-chemistry@ccl.net Fri Jun 17 12:00:00 2011 From: "Michel Petitjean petitjean.chiral()gmail.com" To: CCL Subject: CCL: Algorithm for the point group determination of arbitrary molecules Message-Id: <-44922-110617115820-29942-ITqvJSigFMGb+H7lyUfT+Q%server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 17 Jun 2011 17:58:11 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral_+_gmail.com] Dear Srikanth, In fact you can deduce the point group from the list of graph automorphisms together with their associated isometry, which return DSI values close to zero and CHI values close to zero (both CHI and DSI take values in [0;1]). All that is computed by QCM. For that, you should decide (a) which automorphisms are to be retained, i.e. what are the CHI and DSI values sufficiently close to zero to be retained and (b) write a script which deduce the point group from their associated isometries (the supgroups of automorphisms help, too). The crucial part of the algorithm is (a): strictly null values are inadequate. Some statistics should help to select a cut-off value for DSI and CHI. Best regards, Michel. > ________________________________ > From: Srikanth Patala srikanth.patala ~~ gmail.com > > Dear Michel, > > Thank you very much for your response and the link to the freeware. I also > realized that my question is slightly misleading. I do not yet have a > working code for determination of point group symmetries of arbitrary > molecules (symmetric without deviations). I am still working on it and I > jumped a couple of steps ahead and posted a question about deviation from > symmetries (which is also something that I absolutely require). I am > basically trying to calculate the moment of inertia tensor to determine the > point groups but I am not aware of a good (efficient) algorithm to determine > point symmetries for static, symmetric molecules. Any help with this first > step is also greatly appreciated. > > Thanks, > Srikanth > > On Thu, Jun 16, 2011 at 12:13 PM, Michel Petitjean > petitjean.chiral]~[gmail.com wrote: > > Sent to CCL by: Michel Petitjean [petitjean.chiral!=!gmail.com] > Dear Srikanth, > Such a code would work under the assumption that the symmetry is not > too much distorted. > You may check the deviation from direct symmetry with the direct > symmetry index (DSI) and the deviation from achirality with the chiral > index (CHI), both computable with the QCM freeware: > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > Best regards, > Michel. > > Michel Petitjean > MTi, INSERM UMR-S 973, University Paris 7 > 35 rue Helene Brion, 75205 Paris Cedex 13, France. > Phone: +331 5727 8434; Fax: +331 5727 8372 > E-mail: petitjean.chiral=-=gmail.com (preferred), > michel.petitjean=-=univ-paris-diderot.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.html > > > 2011/6/16 Srikanth Patala srikanth.patala ~~ gmail.com > : >> >> Sent to CCL by: "Srikanth  Patala" [srikanth.patala-*-gmail.com] >> Hello all, >> >> I am trying to write a code to determine the point group of arbitrary >> shapes (clusters of atoms). I am very well aware of all the point symmetries >> and I did find some suggestions online (flowcharts) for developing such a >> code. The main problem now is that I have temperature in my system and hence >> the shape of the clusters fluctuates. I am not sure how to have a code while >> allowing for deviation from symmetric structure. There is an applet online >> that allows for this deviation: >> http://www.colby.edu/chemistry/PChem/scripts/ABC.html >> >> I would like to perform the exact same calculations using a code. Any >> suggestions?? Thanks in advance for your time. >> >> Thanks, >> Srikanth >> From owner-chemistry@ccl.net Fri Jun 17 12:35:00 2011 From: "Srikanth Patala srikanth.patala.#.gmail.com" To: CCL Subject: CCL: Algorithm for the point group determination of arbitrary molecules Message-Id: <-44923-110617122158-10278-F5J5nz2XhaVy5a71LFwYFQ#server.ccl.net> X-Original-From: Srikanth Patala Content-Type: multipart/alternative; boundary=20cf307f34a20a2c9f04a5eac76b Date: Fri, 17 Jun 2011 11:21:07 -0500 MIME-Version: 1.0 Sent to CCL by: Srikanth Patala [srikanth.patala[]gmail.com] --20cf307f34a20a2c9f04a5eac76b Content-Type: text/plain; charset=ISO-8859-1 I was able to find the program. Thank you very much. Srikanth Patala On Fri, Jun 17, 2011 at 5:27 AM, Gustavo Mercier gamercier ~~ yahoo.com < owner-chemistry]![ccl.net> wrote: > Hi! > > You may want to look into this paper... > > Zabrodsky et al. (1993) JACS, 115, 8278-8298 > > It describes a continuous symmetry metric to measure deviations from > idealized point groups. > > A while back Tullio Pilati and Alessandra Forni developed a program they > called Symmol to "symmetrize" coordinates. I believe the program may be in > the ccl archives. If remember correctly, the program required the input of > a tolerance to the deviation from an idealized point group, but did not > require defining the point group to which you would 'symmetrize'. This makes > me believe that the program had an algorithm to define the 'closest' point > group that you may use in your work. > > Look at the following reference: > > Pilati, T. & Forni, A. (1998). *J. Appl. Cryst.* *31* , 503-504 > > Good luck. > > > -- > Gustavo A. Mercier, Jr., MD, PhD > gamercier#,#yahoo.com > Gustavo.Mercier#,#bmc.org > gumercie#,#bu.edu > 617-414-6440 > > > ------------------------------ > *From:* Srikanth Patala srikanth.patala ~~ gmail.com ccl.net> > *To:* "Mercier, Gustavo, " > *Sent:* Thursday, June 16, 2011 4:00 PM > *Subject:* CCL: Algorithm for the point group determination of arbitrary > molecules > > Dear Michel, > > Thank you very much for your response and the link to the freeware. I also > realized that my question is slightly misleading. I do not yet have a > working code for determination of point group symmetries of arbitrary > molecules (symmetric without deviations). I am still working on it and I > jumped a couple of steps ahead and posted a question about deviation from > symmetries (which is also something that I absolutely require). I am > basically trying to calculate the moment of inertia tensor to determine the > point groups but I am not aware of a good (efficient) algorithm to determine > point symmetries for static, symmetric molecules. Any help with this first > step is also greatly appreciated. > > Thanks, > Srikanth > > On Thu, Jun 16, 2011 at 12:13 PM, Michel Petitjean petitjean.chiral]~[ > gmail.com wrote: > > > Sent to CCL by: Michel Petitjean [petitjean.chiral!=!gmail.com] > Dear Srikanth, > Such a code would work under the assumption that the symmetry is not > too much distorted. > You may check the deviation from direct symmetry with the direct > symmetry index (DSI) and the deviation from achirality with the chiral > index (CHI), both computable with the QCM freeware: > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > Best regards, > Michel. > > Michel Petitjean > MTi, INSERM UMR-S 973, University Paris 7 > 35 rue Helene Brion, 75205 Paris Cedex 13, France. > Phone: +331 5727 8434; Fax: +331 5727 8372 > E-mail: petitjean.chiral=-=gmail.com (preferred), > michel.petitjean=-=univ-paris-diderot.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.html > > > 2011/6/16 Srikanth Patala srikanth.patala ~~ gmail.com > : > > > > Sent to CCL by: "Srikanth Patala" [srikanth.patala-*-gmail.com] > > Hello all, > > > > I am trying to write a code to determine the point group of arbitrary > shapes (clusters of atoms). I am very well aware of all the point symmetries > and I did find some suggestions online (flowcharts) for developing such a > code. The main problem now is that I have temperature in my system and hence > the shape of the clusters fluctuates. I am not sure how to have a code while > allowing for deviation from symmetric structure. There is an applet online > that allows for this deviation: > http://www.colby.edu/chemistry/PChem/scripts/ABC.html > > > > I would like to perform the exact same calculations using a code. Any > suggestions?? Thanks in advance for your time. > > > > Thanks, > > Srikanth> > E-mail to subscribers: CHEMISTRY*ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use> > > > > > -- > Srikanth > > > -- Srikanth --20cf307f34a20a2c9f04a5eac76b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I was able to find the program. Thank you very much.

Srikanth Patala=

On Fri, Jun 17, 2011 at 5:27 AM, Gustavo= Mercier gamercier ~~ yahoo.com <owner-chemistry]![ccl= .net> wrote:
Hi!

You may want to look into this paper= ...

Zabrodsky et al. (19= 93) JACS, 115, 8278-8298

It describes a continuous symmetry metric to measure deviations from = idealized point groups.

A while back Tullio Pilati and Aless= andra Forni developed a program they called Symmol to "symmetrize"= ; coordinates. I believe the program may be in the ccl archives. If=A0 reme= mber correctly, the program required the input of a tolerance to the deviat= ion from an idealized point group, but did not require defining the point g= roup to which you would 'symmetrize'. This makes me believe that th= e program had an algorithm to define the 'closest' point group that you may use in your work.

Look at the following reference:

<= /span>
Pilati, T. & Forni, A. (1998). = J. Appl. Cryst. = 31 , 503-504

Good luck.
=A0

--
Gustavo A. Mercier, Jr., MD, PhD
gamercier#,#yahoo.com
Gustavo.Mercier#,#= bmc.org
gumercie#,#bu.edu
617-414-644= 0


From: Srikanth Patala srikanth.patala ~~ gmail.co= m <owner-chemistry#,#cc= l.net>
To: "M= ercier, Gustavo, " <gamercier#,#yahoo.com>
Sent: Thursday, June 16, 201= 1 4:00 PM
Subject: CCL: A= lgorithm for the point group determination of arbitrary molecules

Dear Michel,

Thank you very much for your response and the link to t= he freeware. I also realized that my question is slightly misleading. I do = not yet have a working code for determination of point group symmetries of = arbitrary molecules (symmetric without deviations). I am still working on i= t and I jumped a couple of steps ahead and posted a question about deviatio= n from symmetries (which is also something that I absolutely require). I am= basically trying to calculate the moment of inertia tensor to determine th= e point groups but I am not aware of a good (efficient) algorithm to determ= ine point symmetries for static, symmetric molecules. Any help with this fi= rst step is also greatly appreciated.

Thanks,
Srikanth

On Thu, Jun 16, 2011 at 12:13 PM, Miche= l Petitjean petitjean.chiral]~[gmail.com <owner-chemistry*= ccl.net> wrote:

Sent to CCL by: Michel Petitjean [petitjean.chiral!=3D!gmail.com]
Dear Srikanth,
Such a code would work under the assumption that the symmetry is not
too much distorted.
You may check the deviation from direct symmetry with the direct
symmetry index (DSI) and the deviation from achirality with the chiral
index (CHI), both computable with the QCM freeware:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.h= tml
Best regards,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +33= 1 5727 8372
E-mail: petitjean.chiral=3D-=3Dgmail.com (preferred),
michel.petitjean=3D-=3Duniv-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html


2011/6/16 Srikanth Patala srikanth.patala ~~ gmail.com
<owner-chemistry=3D-=3Dccl.net>:
>
> Sent to CCL by: "Srikanth =A0Patala" [srikanth.patala-*-gmail.com]<= br> > Hello all,
>
> I am trying to write a code to determine the point group of arbitrary = shapes (clusters of atoms). I am very well aware of all the point symmetrie= s and I did find some suggestions online (flowcharts) for developing such a= code. The main problem now is that I have temperature in my system and hen= ce the shape of the clusters fluctuates. I am not sure how to have a code w= hile allowing for deviation from symmetric structure. There is an applet on= line that allows for this deviation: http://www.colby.edu/chemistr= y/PChem/scripts/ABC.html
>
> I would like to perform the exact same calculations using a code. Any = suggestions?? Thanks in advance for your time.
>
> Thanks,
> Srikanth
>



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--
Srikanth


=

--
Srikanth
--20cf307f34a20a2c9f04a5eac76b-- From owner-chemistry@ccl.net Fri Jun 17 19:41:00 2011 From: "Ermias Legges ermiaslegg:-:gmail.com" To: CCL Subject: CCL:G: One electron reduction study using gaussian 09 Message-Id: <-44924-110617165317-30837-8PT+BPRNHDBhRLgHHFbzHA+*+server.ccl.net> X-Original-From: "Ermias Legges" Date: Fri, 17 Jun 2011 16:53:15 -0400 Sent to CCL by: "Ermias Legges" [ermiaslegg : gmail.com] Dear All; I am new to Gaussian package. So please do forgive me if my questions are a bit trivial. I want to study and propose the one electron reduction mechanism for my additives for lithium ion battery. However i am having difficulty in figuring out how to prepare the input file for such geometric optimization. i have tried to run the jobs by simply changing the charge from 0 to -1; but no luck.is there anything i missed? Also, could anyone tell me where I could find examples about how to perform a one electron reduction path way study using Gaussian (with supplementary info about the input file and output files)?