From owner-chemistry@ccl.net Fri Jun 17 07:41:00 2011
From: "Gustavo Mercier gamercier ~~ yahoo.com" <owner-chemistry^server.ccl.net>
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 <gamercier*_*yahoo.com>
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 <owner=
-chemistry/./ccl.net>=0A>To: "Mercier, Gustavo, " <gamercier/./yahoo.co=
m>=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 <owner-ch=
emistry*ccl.net> 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>><owner-chemistry=3D-=3Dccl.net>:=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
<html><body><div style=3D"color:#000; background-color:#fff; font-family:ar=
ial, helvetica, sans-serif;font-size:10pt"><div><span>Hi!</span></div><div>=
<br><span></span></div><div><span>You may want to look into this paper...</=
span></div><div><br><span></span></div><div><span>Zabrodsky et al. (1993) J=
ACS, 115, 8278-8298</span></div><div><br><span></span></div><div><span>It d=
escribes a continuous symmetry metric to measure deviations from idealized =
point groups.</span></div><div><br><span></span></div><div><span>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.</span></div><div><br><span></span></d=
iv><div><span>Look at the following reference:</span></div><div><br><span><=
/span></div><div><font size=3D"3">Pilati, T. & Forni, A. (1998). =
<span class=3D"it"> <i>J. Appl. Cryst.</i> </span> =
<span class=3D"b"> <b>31</b> </span>, 503-504</font>=
</div><div><br></div><div><font size=3D"3">Good luck.<br></font></div><div>=
</div><div><br>--<br>Gustavo A. Mercier, Jr., MD, PhD<br>gamercier/./ya=
hoo.com<br>Gustavo.Mercier/./bmc.org<br>gumercie/./bu.edu<br>617-414-6440<br><b=
r><br><blockquote style=3D"border-left: 2px solid rgb(16, 16, 255); margin-=
left: 5px; padding-left: 5px;"><div style=3D"font-family: arial, helvetica,=
sans-serif; font-size: 10pt;"><div style=3D"font-family: times new roman, =
new york, times, serif; font-size: 12pt;"><font size=3D"2" face=3D"Arial"><=
hr size=3D"1"><b><span style=3D"font-weight:bold;">From:</span></b> Srikant=
h Patala
srikanth.patala ~~ gmail.com <owner-chemistry/./ccl.net><br><b><span s=
tyle=3D"font-weight: bold;">To:</span></b> "Mercier, Gustavo, " <=
;gamercier/./yahoo.com><br><b><span style=3D"font-weight: bold;">Sent:</sp=
an></b> Thursday, June 16, 2011 4:00 PM<br><b><span style=3D"font-weight: b=
old;">Subject:</span></b> CCL: Algorithm for the point group determination =
of arbitrary molecules<br></font><br>=0ADear Michel,<br><br>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.<br>=0A=0A<br>Thanks,<br>Srikanth<br><br><div class=3D"yiv-510987266gmail=
_quote">On Thu, Jun 16, 2011 at 12:13 PM, Michel Petitjean petitjean.chiral=
]~[<a rel=3D"nofollow" target=3D"_blank" href=3D"http://gmail.com">gmail.co=
m</a> <span dir=3D"ltr"><<a rel=3D"nofollow" ymailto=3D"mailto:owner-che=
mistry*ccl.net" target=3D"_blank" href=3D"mailto:owner-chemistry*ccl.net">o=
wner-chemistry*ccl.net</a>></span> wrote:<br>=0A=0A<blockquote class=3D"=
yiv-510987266gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc s=
olid;padding-left:1ex;"><br>=0ASent to CCL by: Michel Petitjean [petitjean.=
chiral!=3D!<a rel=3D"nofollow" target=3D"_blank" href=3D"http://gmail.com">=
gmail.com</a>]<br>=0ADear Srikanth,<br>=0ASuch a code would work under the =
assumption that the symmetry is not<br>=0Atoo much distorted.<br>=0AYou may=
check the deviation from direct symmetry with the direct<br>=0Asymmetry in=
dex (DSI) and the deviation from achirality with the chiral<br>=0Aindex (CH=
I), both computable with the QCM freeware:<br>=0Ahttp://petitjeanmichel.fre=
e.fr/itoweb.petitjean.freeware.html<br>=0ABest regards,<br>=0AMichel.<br>=
=0A<br>=0AMichel Petitjean<br>=0AMTi, INSERM UMR-S 973, University Paris 7<=
br>=0A35 rue Helene Brion, 75205 Paris Cedex 13, France.<br>=0APhone: <a re=
l=3D"nofollow">+331 5727 8434</a>; Fax: <a rel=3D"nofollow">+331 5727 8372<=
/a><br>=0AE-mail: petitjean.chiral=3D-=3D<a rel=3D"nofollow" target=3D"_bla=
nk" href=3D"http://gmail.com">gmail.com</a> (preferred),<br>=0Amichel.petit=
jean=3D-=3D<a rel=3D"nofollow" target=3D"_blank" href=3D"http://univ-paris-=
diderot.fr">univ-paris-diderot.fr</a><br>=0Ahttp://petitjeanmichel.free.fr/=
itoweb.petitjean.html<br>=0A<br>=0A<br>=0A2011/6/16 Srikanth Patala srikant=
h.patala ~~ <a rel=3D"nofollow" target=3D"_blank" href=3D"http://gmail.com"=
>gmail.com</a><br>=0A<owner-chemistry=3D-=3D<a rel=3D"nofollow" target=
=3D"_blank" href=3D"http://ccl.net">ccl.net</a>>:<br>=0A<div><div></div>=
<div class=3D"yiv-510987266h5">><br>=0A> Sent to CCL by: "Srikanth &n=
bsp;Patala" [srikanth.patala-*-<a rel=3D"nofollow" target=3D"_blank" href=
=3D"http://gmail.com">gmail.com</a>]<br>=0A> Hello all,<br>=0A><br>=
=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<br>=0A=0A=0A><br>=0A> I would like to perform the =
exact same calculations using a code. Any suggestions?? Thanks in advance f=
or your time.<br>=0A><br>=0A> Thanks,<br>=0A> Srikanth<br>=0A><=
br>=0A<br>=0A<br>=0A<br>=0A-=3D This is automatically added to each message=
by the mailing script =3D-<br>=0A<br>=0AE-mail to subscribers: <a rel=3D"n=
ofollow" ymailto=3D"mailto:CHEMISTRY*ccl.net" target=3D"_blank" href=3D"mai=
lto:CHEMISTRY*ccl.net">CHEMISTRY*ccl.net</a> or use:<br>=0A &=
nbsp;http://www.ccl.net/cgi-bin/ccl/send_ccl_message<br>=0A<br>=0AE-mail to=
administrators: <a rel=3D"nofollow" ymailto=3D"mailto:CHEMISTRY-REQUEST*cc=
l.net" target=3D"_blank" href=3D"mailto:CHEMISTRY-REQUEST*ccl.net">CHEMISTR=
Y-REQUEST*ccl.net</a> or use<br>=0A <a rel=3D"nofollow"=
target=3D"_blank" href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message"=
>http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>=0A<br>=0ASubscribe=
/Unsubscribe:<br>=0A http://www.ccl.net/chemistry/sub_u=
nsub.shtml<br>=0A<br>=0ABefore posting, check wait time at: http://www.ccl.=
net<br>=0A<br>=0AJob: http://www.ccl.net/jobs<br>=0AConferences: http://ser=
ver.ccl.net/chemistry/announcements/conferences/<br>=0A<br>=0ASearch Messag=
es: http://www.ccl.net/chemistry/searchccl/index.shtml<br>=0A<br>=0A =
http://www.ccl.net/spammers.txt<br>=0A<br>=0ARTFI: http://www=
.ccl.net/chemistry/aboutccl/instructions/<br>=0A<br>=0A<br>=0A</div></div><=
/blockquote></div><br><br clear=3D"all"><br>-- <br>Srikanth<br><br><br></di=
v></div></blockquote></div></div></body></html>
--0-677089790-1308306449=:67836--
From owner-chemistry@ccl.net Fri Jun 17 08:15:01 2011
From: "Jens Spanget-Larsen spanget.%%.ruc.dk" <owner-chemistry%%server.ccl.net>
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 <spanget:-:ruc.dk>
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
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
<title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
<font size="-1"><font face="Courier New, Courier, monospace"><br>
Dear Gustavo,<br>
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). <br>
Jens >--<<br>
</font></font>
<pre class="moz-signature" cols="72"> ------------------------------------------------------
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: <a class="moz-txt-link-abbreviated" href="mailto:spanget!A!ruc.dk">spanget!A!ruc.dk</a>
DK-4000 Roskilde, Denmark <a class="moz-txt-link-freetext" href="http://www.ruc.dk/~spanget">http://www.ruc.dk/~spanget</a>
------------------------------------------------------</pre>
<br>
On 6/16/2011 19:30, Gustavo L.C. Moura gustavo.moura^ufpe.br wrote:
<blockquote
cite="mid:-id%233dt-44913-110616133031-26753-oaST1ZfkIX5ERrKFo8gb9g!A!server.ccl.net"
type="cite">
<pre wrap="">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: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY!A!ccl.net">CHEMISTRY!A!ccl.net</a> or use:
<a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>
E-mail to administrators: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY-REQUEST!A!ccl.net">CHEMISTRY-REQUEST!A!ccl.net</a> or use
<a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a<a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a>
Before posting, check wait time at: <a class="moz-txt-link-freetext" href="http://www.ccl.net">http://www.ccl.net</a>
Job: <a class="moz-txt-link-freetext" href="http://www.ccl.net/jobs">http://www.ccl.net/jobs</a>
Conferences: <a class="moz-txt-link-freetext" href="http://server.ccl.net/chemistry/announcements/conferences/">http://server.ccl.net/chemistry/announcements/conferences/</a>
Search Messages: <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/searchccl/index.shtml">http://www.ccl.net/chemistry/searchccl/index.shtml</a<a class="moz-txt-link-freetext" href="http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a>
RTFI: <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a>
</pre>
</blockquote>
</body>
</html>
--------------020604020705020502050601--
From owner-chemistry@ccl.net Fri Jun 17 08:51:01 2011
From: "Serdar Badoglu sbadoglu{}gazi.edu.tr" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: band deconvolution
Message-Id: <-44920-110617062608-14885-ELjJR76Jei49Qp0WTL0ytw%server.ccl.net>
X-Original-From: "Serdar Badoglu" <sbadoglu::gazi.edu.tr>
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" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: J. C. Rayez THEOCHEM Special Issue
Message-Id: <-44921-110617104643-16858-28jAhrJ5nLTlKcgrUUhRcQ**server.ccl.net>
X-Original-From: "Andrea Lombardi" <ebiu2005],[gmail.com>
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" <owner-chemistry%server.ccl.net>
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 <petitjean.chiral|*|gmail.com>
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 <owner-chemistry*ccl.net> 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
> <owner-chemistry=-=ccl.net>:
>>
>> 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" <owner-chemistry#server.ccl.net>
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 <srikanth.patala-*-gmail.com>
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 <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
>
> 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 <owner-chemistry*ccl.net> 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
> <owner-chemistry=-=ccl.net>:
> >
> > 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.<br><br>Srikanth Patala=
<br><br><div class=3D"gmail_quote">On Fri, Jun 17, 2011 at 5:27 AM, Gustavo=
Mercier gamercier ~~ <a href=3D"http://yahoo.com">yahoo.com</a> <span dir=
=3D"ltr"><<a href=3D"mailto:owner-chemistry]![ccl.net">owner-chemistry]![ccl=
.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><div><div style=3D"color:#000;background-co=
lor:#fff;font-family:arial, helvetica, sans-serif;font-size:10pt"><div><spa=
n>Hi!</span></div>
<div><br><span></span></div><div><span>You may want to look into this paper=
...</span></div><div><br><span></span></div><div><span>Zabrodsky et al. (19=
93) JACS, 115, 8278-8298</span></div><div><br><span></span></div><div>
<span>It describes a continuous symmetry metric to measure deviations from =
idealized point groups.</span></div>
<div><br><span></span></div><div><span>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.</span></div><div><br><span></span></d=
iv><div><span>Look at the following reference:</span></div><div><br><span><=
/span></div><div><font size=3D"3">Pilati, T. & Forni, A. (1998). =
<span> <i>J. Appl. Cryst.</i> </span> <span> =
<b>31</b> </span>, 503-504</font></div>
<div><br></div><div><font size=3D"3">Good luck.<br></font></div><div>=A0</d=
iv><div><br>--<br>Gustavo A. Mercier, Jr., MD, PhD<br>gamercier#,#<a href=
=3D"http://yahoo.com" target=3D"_blank">yahoo.com</a><br>Gustavo.Mercier#,#=
<a href=3D"http://bmc.org" target=3D"_blank">bmc.org</a><br>
gumercie#,#<a href=3D"http://bu.edu" target=3D"_blank">bu.edu</a><br><a hre=
f=3D"tel:617-414-6440" value=3D"+16174146440" target=3D"_blank">617-414-644=
0</a><br><br><br><blockquote style=3D"border-left:2px solid rgb(16, 16, 255=
);margin-left:5px;padding-left:5px">
<div style=3D"font-family:arial, helvetica, sans-serif;font-size:10pt"><div=
style=3D"font-family:times new roman, new york, times, serif;font-size:12p=
t"><font size=3D"2" face=3D"Arial"><hr size=3D"1"><b><span style=3D"font-we=
ight:bold">From:</span></b> Srikanth Patala
srikanth.patala ~~ <a href=3D"http://gmail.com" target=3D"_blank">gmail.co=
m</a> <owner-chemistry#,#<a href=3D"http://ccl.net" target=3D"_blank">cc=
l.net</a>><br><b><span style=3D"font-weight:bold">To:</span></b> "M=
ercier, Gustavo, " <gamercier#,#<a href=3D"http://yahoo.com" target=
=3D"_blank">yahoo.com</a>><br>
<b><span style=3D"font-weight:bold">Sent:</span></b> Thursday, June 16, 201=
1 4:00 PM<br><b><span style=3D"font-weight:bold">Subject:</span></b> CCL: A=
lgorithm for the point group determination of arbitrary molecules<br></font=
><br>
Dear Michel,<br><br>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.<br>
<br>Thanks,<br>Srikanth<br><br><div>On Thu, Jun 16, 2011 at 12:13 PM, Miche=
l Petitjean petitjean.chiral]~[<a rel=3D"nofollow" href=3D"http://gmail.com=
" target=3D"_blank">gmail.com</a> <span dir=3D"ltr"><<a rel=3D"nofollow"=
href=3D"mailto:owner-chemistry*ccl.net" target=3D"_blank">owner-chemistry*=
ccl.net</a>></span> wrote:<br>
<blockquote style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-l=
eft:1ex"><br>
Sent to CCL by: Michel Petitjean [petitjean.chiral!=3D!<a rel=3D"nofollow" =
href=3D"http://gmail.com" target=3D"_blank">gmail.com</a>]<br>
Dear Srikanth,<br>
Such a code would work under the assumption that the symmetry is not<br>
too much distorted.<br>
You may check the deviation from direct symmetry with the direct<br>
symmetry index (DSI) and the deviation from achirality with the chiral<br>
index (CHI), both computable with the QCM freeware:<br>
<a href=3D"http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html" t=
arget=3D"_blank">http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.h=
tml</a><br>
Best regards,<br>
Michel.<br>
<br>
Michel Petitjean<br>
MTi, INSERM UMR-S 973, University Paris 7<br>
35 rue Helene Brion, 75205 Paris Cedex 13, France.<br>
Phone: <a rel=3D"nofollow">+331 5727 8434</a>; Fax: <a rel=3D"nofollow">+33=
1 5727 8372</a><br>
E-mail: petitjean.chiral=3D-=3D<a rel=3D"nofollow" href=3D"http://gmail.com=
" target=3D"_blank">gmail.com</a> (preferred),<br>
michel.petitjean=3D-=3D<a rel=3D"nofollow" href=3D"http://univ-paris-didero=
t.fr" target=3D"_blank">univ-paris-diderot.fr</a><br>
<a href=3D"http://petitjeanmichel.free.fr/itoweb.petitjean.html" target=3D"=
_blank">http://petitjeanmichel.free.fr/itoweb.petitjean.html</a><br>
<br>
<br>
2011/6/16 Srikanth Patala srikanth.patala ~~ <a rel=3D"nofollow" href=3D"ht=
tp://gmail.com" target=3D"_blank">gmail.com</a><br>
<owner-chemistry=3D-=3D<a rel=3D"nofollow" href=3D"http://ccl.net" targe=
t=3D"_blank">ccl.net</a>>:<br>
<div><div></div><div>><br>
> Sent to CCL by: "Srikanth =A0Patala" [srikanth.patala-*-<a r=
el=3D"nofollow" href=3D"http://gmail.com" target=3D"_blank">gmail.com</a>]<=
br>
> Hello all,<br>
><br>
> 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: <a href=3D"http://www.colby.edu/chemis=
try/PChem/scripts/ABC.html" target=3D"_blank">http://www.colby.edu/chemistr=
y/PChem/scripts/ABC.html</a><br>
><br>
> I would like to perform the exact same calculations using a code. Any =
suggestions?? Thanks in advance for your time.<br>
><br>
> Thanks,<br>
> Srikanth<br>
><br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br>
<br>
E-mail to subscribers: <a rel=3D"nofollow" href=3D"mailto:CHEMISTRY*ccl.net=
" target=3D"_blank">CHEMISTRY*ccl.net</a> or use:<br>
=A0 =A0 =A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" tar=
get=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a><br>
<br>
E-mail to administrators: <a rel=3D"nofollow" href=3D"mailto:CHEMISTRY-REQU=
EST*ccl.net" target=3D"_blank">CHEMISTRY-REQUEST*ccl.net</a> or use<br>
=A0 =A0 =A0<a rel=3D"nofollow" href=3D"http://www.ccl.net/cgi-bin/ccl/send=
_ccl_message" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage</a><br>
<br>
Subscribe/Unsubscribe:<br>
=A0 =A0 =A0<a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=
=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br>
=A0 =A0 =A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank">h=
ttp://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</div></div></blockquote></div><br><br clear=3D"all"><br>-- <br>Srikanth<br=
><br><br></div></div></blockquote></div></div></div></blockquote></div><br>=
<br clear=3D"all"><br>-- <br>Srikanth<br>
--20cf307f34a20a2c9f04a5eac76b--
From owner-chemistry@ccl.net Fri Jun 17 19:41:00 2011
From: "Ermias Legges ermiaslegg:-:gmail.com" <owner-chemistry+*+server.ccl.net>
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" <ermiaslegg:+:gmail.com>
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)?