From owner-chemistry@ccl.net Sat Nov 21 04:27:01 2009
From: "Adam Kubas adam.kubas]*[kit.edu" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: Which program to optimize the crystal structure of transition metal complex?
Message-Id: <-40737-091121041925-22946-HVHmSqU/0XKcEjNkXQkdcw,+,server.ccl.net>
X-Original-From: Adam Kubas <adam.kubas+*+kit.edu>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=ISO-8859-1
Date: Sat, 21 Nov 2009 09:27:39 +0100
MIME-Version: 1.0


Sent to CCL by: Adam Kubas [adam.kubas^kit.edu]
Dear Mariusz,

My propositions are Turbomole and Orca - first is the fastest DFT code
I've ever seen with wide range of options to control spin state of
optimized compound but you have to buy it (free demo is available).
The second program is a free package and is easily to use.

2009/11/20 Mariusz Radon mariusz.radon(0)gmail.com <owner-chemistry a ccl.net=
>:
>
> Sent to CCL by: Mariusz Radon [mariusz.radon]-[gmail.com]
> Dear Colleagues,
>
> I am looking for a program being able to optimize the crystal
> structure of transition metal complex (molecular structure and unit
> cell parameters) at DFT level. An important point is that I must be
> able to control the spin state of the complex, because I would like to
> perform such optimizations for different spin states in order to
> capture the influence of the spin state on the molecular structure and
> packing in the crystal.
>
> Could you recommend me any program capable to achieve this goal
> (preferably, but not necessarily free software)? Thank you in advance
> very much.
>
> Best regards,
> Mariusz Radon


--=20
Adam Kubas
Karlsruher Institut f=FCr Technologie (KIT)
Institut f=FCr Physikalische Chemie
Abteilung f=FCr Theoretische Chemie
Geb. 30.45, Kaiserstra=DFe 12, D-76131 Karlsruhe
http://www.ipc.uni-karlsruhe.de/theochem/
----------------------------------------------------------------------
Office:
Institut f=FCr Nanotechnologie
Raum: 640/0-333
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Tel.: +49 7247 82-8834
http://www.int.kit.edu

KIT - Universit=E4t des Landes Baden-W=FCrttemberg und
nationales Gro=DFforschungszentrum in der Helmholtz-Gemeinschaft


From owner-chemistry@ccl.net Sat Nov 21 10:28:01 2009
From: "qiancheng shen qianchengshen{:}gmail.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: How can I find the HOMO from the MOPAC output??
Message-Id: <-40738-091121000011-28367-su1D+iQtcIDN32QDg+OSuQ[A]server.ccl.net>
X-Original-From: qiancheng shen <qianchengshen-x-gmail.com>
Content-Type: multipart/alternative; boundary=0016e640d1f03eeb0f0478d98895
Date: Sat, 21 Nov 2009 11:53:15 +0800
MIME-Version: 1.0


Sent to CCL by: qiancheng shen [qianchengshen^gmail.com]
--0016e640d1f03eeb0f0478d98895
Content-Type: text/plain; charset=ISO-8859-1

Dear CCLers,
        I got a MOPAC output file will all EIGENVECTORS printed out. But,
Which Molecular Orbital is the HOMO?
        Could anyone help me?

        The output MO information looks like:

        Root No.    1       2       3       4       5       6       7
8

              1 A     2 A     3 A     4 A     5 A     6 A     7 A     8 A

           -37.523 -35.473 -32.665 -29.061 -25.420 -22.108 -20.717 -19.976

  S   C  1 -0.1694 -0.2922 -0.3855 -0.3662  0.2965 -0.1799 -0.2729  0.1466
  Px  C  1 -0.0710 -0.1061 -0.1044 -0.0410 -0.0398  0.0921  0.2435 -0.1648
  Py  C  1 -0.0125 -0.0125  0.0008  0.0230 -0.0359  0.0378 -0.0719  0.0727
  Pz  C  1 -0.0016 -0.0004  0.0022  0.0022  0.0032 -0.0147  0.0045 -0.0002
  S   C  2 -0.2852 -0.3992 -0.3553 -0.1230 -0.0803  0.1349  0.3741 -0.2315
  Px  C  2 -0.0130  0.0324  0.1300  0.2048 -0.1953  0.0878  0.1430 -0.0600
  Py  C  2 -0.0619 -0.0591  0.0039  0.0897 -0.1163  0.0882 -0.1543  0.1498
.........
and  Root No.    9      10      11      12      13      14      15      16

              9 A    10 A    11 A    12 A    13 A    14 A    15 A    16 A

           -16.372 -15.825 -15.103 -14.911 -14.409 -13.993 -13.166 -12.837

  S   C  1  0.0584  0.0193 -0.0318 -0.0135 -0.0222 -0.0010 -0.0170  0.0373
  Px  C  1 -0.1888 -0.0755  0.3150  0.1065  0.2760 -0.1557 -0.1153  0.2238
  Py  C  1 -0.2164  0.2561  0.2688 -0.0859 -0.2704  0.0105 -0.0940  0.0989
  Pz  C  1 -0.0448 -0.0097 -0.0142 -0.0804  0.0208  0.0267 -0.1218 -0.0939

--0016e640d1f03eeb0f0478d98895
Content-Type: text/html; charset=ISO-8859-1
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Dear CCLers,<br>=A0=A0=A0=A0=A0=A0=A0 I got a MOPAC output file will all EI=
GENVECTORS printed out. But, Which Molecular Orbital is the HOMO?<br>=A0=A0=
=A0=A0=A0=A0=A0 Could anyone help me? <br><br>=A0=A0=A0=A0=A0=A0=A0 The out=
put MO information looks like:<br>=A0=A0=A0=A0=A0=A0=A0=A0 <br>
=A0=A0=A0=A0=A0=A0=A0 Root No.=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=
=A0=A0 3=A0=A0=A0=A0=A0=A0 4=A0=A0=A0=A0=A0=A0 5=A0=A0=A0=A0=A0=A0 6=A0=A0=
=A0=A0=A0=A0 7=A0=A0=A0=A0=A0=A0 8<br><br>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0 1 A=A0=A0=A0=A0 2 A=A0=A0=A0=A0 3 A=A0=A0=A0=A0 4 A=A0=A0=A0=A0 5 A=
=A0=A0=A0=A0 6 A=A0=A0=A0=A0 7 A=A0=A0=A0=A0 8 A=A0=A0 <br><br>=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0 -37.523 -35.473 -32.665 -29.061 -25.420 -22.108 -20.717 =
-19.976<br>
=A0 <br>=A0 S=A0=A0 C=A0 1 -0.1694 -0.2922 -0.3855 -0.3662=A0 0.2965 -0.179=
9 -0.2729=A0 0.1466<br>=A0 Px=A0 C=A0 1 -0.0710 -0.1061 -0.1044 -0.0410 -0.=
0398=A0 0.0921=A0 0.2435 -0.1648<br>=A0 Py=A0 C=A0 1 -0.0125 -0.0125=A0 0.0=
008=A0 0.0230 -0.0359=A0 0.0378 -0.0719=A0 0.0727<br>
=A0 Pz=A0 C=A0 1 -0.0016 -0.0004=A0 0.0022=A0 0.0022=A0 0.0032 -0.0147=A0 0=
.0045 -0.0002<br>=A0 S=A0=A0 C=A0 2 -0.2852 -0.3992 -0.3553 -0.1230 -0.0803=
=A0 0.1349=A0 0.3741 -0.2315<br>=A0 Px=A0 C=A0 2 -0.0130=A0 0.0324=A0 0.130=
0=A0 0.2048 -0.1953=A0 0.0878=A0 0.1430 -0.0600<br>
=A0 Py=A0 C=A0 2 -0.0619 -0.0591=A0 0.0039=A0 0.0897 -0.1163=A0 0.0882 -0.1=
543=A0 0.1498<br>.........<br>and=A0 Root No.=A0=A0=A0 9=A0=A0=A0=A0=A0 10=
=A0=A0=A0=A0=A0 11=A0=A0=A0=A0=A0 12=A0=A0=A0=A0=A0 13=A0=A0=A0=A0=A0 14=A0=
=A0=A0=A0=A0 15=A0=A0=A0=A0=A0 16<br><br>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0 9 A=A0=A0=A0 10 A=A0=A0=A0 11 A=A0=A0=A0 12 A=A0=A0=A0 13 A=A0=A0=A0=
 14 A=A0=A0=A0 15 A=A0=A0=A0 16 A=A0=A0 <br>
<br>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -16.372 -15.825 -15.103 -14.911 -14.409 =
-13.993 -13.166 -12.837<br>=A0 <br>=A0 S=A0=A0 C=A0 1=A0 0.0584=A0 0.0193 -=
0.0318 -0.0135 -0.0222 -0.0010 -0.0170=A0 0.0373<br>=A0 Px=A0 C=A0 1 -0.188=
8 -0.0755=A0 0.3150=A0 0.1065=A0 0.2760 -0.1557 -0.1153=A0 0.2238<br>
=A0 Py=A0 C=A0 1 -0.2164=A0 0.2561=A0 0.2688 -0.0859 -0.2704=A0 0.0105 -0.0=
940=A0 0.0989<br>=A0 Pz=A0 C=A0 1 -0.0448 -0.0097 -0.0142 -0.0804=A0 0.0208=
=A0 0.0267 -0.1218 -0.0939<br><br><br>

--0016e640d1f03eeb0f0478d98895--


From owner-chemistry@ccl.net Sat Nov 21 11:19:00 2009
From: "Morad El-Hendawy m80elhendawy*|*yahoo.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: How can I find the HOMO from the MOPAC output??
Message-Id: <-40739-091121111808-31321-Pz8wOHYgfJQn7t7vbQMueA() server.ccl.net>
X-Original-From: Morad El-Hendawy <m80elhendawy[A]yahoo.com>
Content-Type: multipart/alternative; boundary="0-2092961422-1258820274=:21464"
Date: Sat, 21 Nov 2009 08:17:54 -0800 (PST)
MIME-Version: 1.0


Sent to CCL by: Morad El-Hendawy [m80elhendawy*_*yahoo.com]
--0-2092961422-1258820274=:21464
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Qiancheng,
Go to Berif outpout, you will foind a summary like below:=20

FINAL HEAT OF FORMATION =3D 26.97779 KCAL
TOTAL ENERGY =3D -19.78933 EV
ELECTRONIC ENERGY =3D -27.20810 EV
CORE-CORE REPULSION =3D 7.41878 EV
IONIZATION POTENTIAL =3D 8.38124
NO. OF FILLED LEVELS =3D 1
MOLECULAR WEIGHT =3D 7.948

> From the value of ionization potential you can specify the HOMO level; beca=
use the former is negative value of the later. See this representative exam=
ple for LiH molecule:

TOTAL ENERGY =3D -19.78933 EV
ELECTRONIC ENERGY =3D -27.20810 EV
CORE-CORE REPULSION =3D 7.41878 EV
IONIZATION POTENTIAL =3D 8.38124
NO. OF FILLED LEVELS =3D 1
MOLECULAR WEIGHT =3D 7.948
EIGENVECTORS
ROOT NO. 1=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 4=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0 5
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -8.38124=A0 0.63258=A0=A0 2.4=
5221=A0=A0 2.45221 =A0=A0 5.60161

S Li=A0=A0=A0=A0 1=A0=A0=A0 0.41230=A0=A0 0.80110=A0=A0 0.00000=A0 0.00000=
=A0 -0.43387
PX Li=A0=A0 1 =A0=A0 0.34007 =A0 -0.57714=A0 0.00000=A0 0.00000=A0 -0.74247
PY Li =A0 1 =A0=A0 0.00000=A0=A0 0.00000=A0 -0.92376=A0 0.38298=A0 0.00000
PZ Li=A0=A0 1 =A0=A0 0.00000=A0=A0 0.00000=A0=A0 0.38298=A0 0.92376=A0=A0 0=
.00000

Best regards
***************************************************************************=
***********************Morad M. El-HendawyIreland
***************************************************************************=
***********************=A0If you want a happy life, do four things:=A01- Co=
ntemplate and be thankful,
2- The past is gone forever,
3- Today all that you have,
4- Leave the future alone until it come.=A0********************************=
***************************************************************************=
********

--- On Sat, 11/21/09, qiancheng shen qianchengshen{:}gmail.com <owner-chemi=
stry]~[ccl.net> wrote:

> From: qiancheng shen qianchengshen{:}gmail.com <owner-chemistry]~[ccl.net>
Subject: CCL: How can I find the HOMO from the MOPAC output??
To: "El-Hendawy, Morad Metwally " <m80elhendawy]~[yahoo.com>
Date: Saturday, November 21, 2009, 5:53 AM

Dear CCLers,
=A0=A0=A0=A0=A0=A0=A0 I got a MOPAC output file will all EIGENVECTORS print=
ed out. But, Which Molecular Orbital is the HOMO?
=A0=A0=A0=A0=A0=A0=A0 Could anyone help me?=20

=A0=A0=A0=A0=A0=A0=A0 The output MO information looks like:
=A0=A0=A0=A0=A0=A0=A0=A0=20
=0A=A0=A0=A0=A0=A0=A0=A0 Root No.=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=
=A0=A0=A0 3=A0=A0=A0=A0=A0=A0 4=A0=A0=A0=A0=A0=A0 5=A0=A0=A0=A0=A0=A0 6=A0=
=A0=A0=A0=A0=A0 7=A0=A0=A0=A0=A0=A0 8

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1 A=A0=A0=A0=A0 2 A=A0=A0=A0=A0 3 A=
=A0=A0=A0=A0 4 A=A0=A0=A0=A0 5 A=A0=A0=A0=A0 6 A=A0=A0=A0=A0 7 A=A0=A0=A0=
=A0 8 A=A0=A0=20

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -37.523 -35.473 -32.665 -29.061 -25.420 -22.=
108 -20.717 -19.976
=0A=A0=20
=A0 S=A0=A0 C=A0 1 -0.1694 -0.2922 -0.3855 -0.3662=A0 0.2965 -0.1799 -0.272=
9=A0 0.1466
=A0 Px=A0 C=A0 1 -0.0710 -0.1061 -0.1044 -0.0410 -0.0398=A0 0.0921=A0 0.243=
5 -0.1648
=A0 Py=A0 C=A0 1 -0.0125 -0.0125=A0 0.0008=A0 0.0230 -0.0359=A0 0.0378 -0.0=
719=A0 0.0727
=0A=A0 Pz=A0 C=A0 1 -0.0016 -0.0004=A0 0.0022=A0 0.0022=A0 0.0032 -0.0147=
=A0 0.0045 -0.0002
=A0 S=A0=A0 C=A0 2 -0.2852 -0.3992 -0.3553 -0.1230 -0.0803=A0 0.1349=A0 0.3=
741 -0.2315
=A0 Px=A0 C=A0 2 -0.0130=A0 0.0324=A0 0.1300=A0 0.2048 -0.1953=A0 0.0878=A0=
 0.1430 -0.0600
=0A=A0 Py=A0 C=A0 2 -0.0619 -0.0591=A0 0.0039=A0 0.0897 -0.1163=A0 0.0882 -=
0.1543=A0 0.1498
.........
and=A0 Root No.=A0=A0=A0 9=A0=A0=A0=A0=A0 10=A0=A0=A0=A0=A0 11=A0=A0=A0=A0=
=A0 12=A0=A0=A0=A0=A0 13=A0=A0=A0=A0=A0 14=A0=A0=A0=A0=A0 15=A0=A0=A0=A0=A0=
 16

=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 9 A=A0=A0=A0 10 A=A0=A0=A0 11 A=A0=
=A0=A0 12 A=A0=A0=A0 13 A=A0=A0=A0 14 A=A0=A0=A0 15 A=A0=A0=A0 16 A=A0=A0=
=20
=0A
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -16.372 -15.825 -15.103 -14.911 -14.409 -13.=
993 -13.166 -12.837
=A0=20
=A0 S=A0=A0 C=A0 1=A0 0.0584=A0 0.0193 -0.0318 -0.0135 -0.0222 -0.0010 -0.0=
170=A0 0.0373
=A0 Px=A0 C=A0 1 -0.1888 -0.0755=A0 0.3150=A0 0.1065=A0 0.2760 -0.1557 -0.1=
153=A0 0.2238
=0A=A0 Py=A0 C=A0 1 -0.2164=A0 0.2561=A0 0.2688 -0.0859 -0.2704=A0 0.0105 -=
0.0940=A0 0.0989
=A0 Pz=A0 C=A0 1 -0.0448 -0.0097 -0.0142 -0.0804=A0 0.0208=A0 0.0267 -0.121=
8 -0.0939


=0A=0A=0A=0A      
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<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;">Dear Qiancheng,<br>Go to Berif outpout, you w=
ill foind a summary like below: <br><br>FINAL HEAT OF FORMATION =3D 26.9777=
9 KCAL<br>TOTAL ENERGY =3D -19.78933 EV<br>ELECTRONIC ENERGY =3D -27.20810 =
EV<br>CORE-CORE REPULSION =3D 7.41878 EV<br>IONIZATION POTENTIAL =3D 8.3812=
4<br>NO. OF FILLED LEVELS =3D 1<br>MOLECULAR WEIGHT =3D 7.948<br><br>From t=
he value of ionization potential you can specify the HOMO level; because th=
e former is negative value of the later. See this representative example fo=
r LiH molecule:<br><br>TOTAL ENERGY =3D -19.78933 EV<br>ELECTRONIC ENERGY =
=3D -27.20810 EV<br>CORE-CORE REPULSION =3D 7.41878 EV<br>IONIZATION POTENT=
IAL =3D <span style=3D"background-color: rgb(255, 255, 0);">8.38124</span><=
br>NO. OF FILLED LEVELS =3D 1<br>MOLECULAR WEIGHT =3D 7.948<br>EIGENVECTORS=
<br>ROOT NO. 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;
 2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5<br>&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;<span style=3D"background-color: rgb(255, 255, 0);"> -8.38124</=
span>&nbsp; 0.63258&nbsp;&nbsp; 2.45221&nbsp;&nbsp; 2.45221 &nbsp;&nbsp; 5.=
60161<br><br>S Li&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp; 0.41230&nbsp;=
&nbsp; 0.80110&nbsp;&nbsp; 0.00000&nbsp; 0.00000&nbsp; -0.43387<br>PX Li&nb=
sp;&nbsp; 1 &nbsp;&nbsp; 0.34007 &nbsp; -0.57714&nbsp; 0.00000&nbsp; 0.0000=
0&nbsp; -0.74247<br>PY Li &nbsp; 1 &nbsp;&nbsp; 0.00000&nbsp;&nbsp; 0.00000=
&nbsp; -0.92376&nbsp; 0.38298&nbsp; 0.00000<br>PZ Li&nbsp;&nbsp; 1 &nbsp;&n=
bsp; 0.00000&nbsp;&nbsp; 0.00000&nbsp;&nbsp; 0.38298&nbsp; 0.92376&nbsp;&nb=
sp; 0.00000<br><br><div>Best regards<br><strong><font
 color=3D"#00407f"><font style=3D"background-color: rgb(230, 230, 230);" fa=
ce=3D"arial, helvetica, sans-serif" size=3D"4">****************************=
**********************************************************************</fon=
t></font></strong></div><div><strong><font color=3D"#00407f"><font style=3D=
"background-color: rgb(230, 230, 230);" face=3D"arial, helvetica, sans-seri=
f">Morad M. El-Hendawy</font></font></strong></div><span style=3D"text-deco=
ration: underline;"><span style=3D"font-weight: bold;">Ireland</span></span=
><br><div><strong><font style=3D"background-color: rgb(230, 230, 230);" col=
or=3D"#00407f" face=3D"Arial" size=3D"4">**********************************=
****************************************************************</font></st=
rong></div><div><strong><font style=3D"background-color: rgb(230, 230, 230)=
;" color=3D"#00407f"></font></strong><font size=3D"4">&nbsp;</font><strong>=
<font style=3D"background-color: rgb(255, 128, 255);" color=3D"#000000" fac=
e=3D"arial, helvetica,
 sans-serif" size=3D"4">If you want a happy life, do four things:</font></s=
trong></div><div><strong><font color=3D"#00407f"><font style=3D"background-=
color: rgb(230, 230, 230);"></font></font></strong><font face=3D"arial, hel=
vetica, sans-serif" size=3D"4">&nbsp;</font></div><div><strong><font color=
=3D"#00407f"><font style=3D"background-color: rgb(230, 230, 230);" color=3D=
"#373e68" face=3D"arial, helvetica, sans-serif">1- Contemplate and be thank=
ful,<br></font><font face=3D"arial, helvetica, sans-serif"><font style=3D"b=
ackground-color: rgb(230, 230, 230);"><font color=3D"#373e68">2- The past i=
s gone forever,<br>3- Today all that you have,<br>4- Leave the future alone=
 until it come.</font>&nbsp;</font></font></font></strong></div><div><stron=
g><font style=3D"background-color: rgb(230, 230, 230);" color=3D"#00407f" f=
ace=3D"Arial">*************************************************************=
******************************************************</font></strong></div=
><img
 alt=3D""><strong></strong><br><br>--- On <b>Sat, 11/21/09, qiancheng shen =
qianchengshen{:}gmail.com <i>&lt;owner-chemistry]~[ccl.net&gt;</i></b> wrote:=
<br><blockquote style=3D"border-left: 2px solid rgb(16, 16, 255); margin-le=
ft: 5px; padding-left: 5px;"><br>From: qiancheng shen qianchengshen{:}gmail=
.com &lt;owner-chemistry]~[ccl.net&gt;<br>Subject: CCL: How can I find the HO=
MO from the MOPAC output??<br>To: "El-Hendawy, Morad Metwally " &lt=
;m80elhendawy]~[yahoo.com&gt;<br>Date: Saturday, November 21, 2009, 5:53 AM<b=
r><br><div id=3D"yiv165989015">Dear CCLers,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp; I got a MOPAC output file will all EIGENVECTORS printed out.=
 But, Which Molecular Orbital is the HOMO?<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp; Could anyone help me? <br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp; The output MO information looks like:<br>&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp; <br>=0A&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
; Root No.&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8<br>=
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp; 1 A&nbsp;&nbsp;&nbsp;&nbsp; 2 A&nbsp;&nbsp;&nbsp;&nbsp; 3 A&nbsp;&n=
bsp;&nbsp;&nbsp; 4 A&nbsp;&nbsp;&nbsp;&nbsp; 5 A&nbsp;&nbsp;&nbsp;&nbsp; 6 =
A&nbsp;&nbsp;&nbsp;&nbsp; 7 A&nbsp;&nbsp;&nbsp;&nbsp; 8 A&nbsp;&nbsp; <br><=
br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -37.523 -35=
.473 -32.665 -29.061 -25.420 -22.108 -20.717 -19.976<br>=0A&nbsp; <br>&nbsp=
; S&nbsp;&nbsp; C&nbsp; 1 -0.1694 -0.2922 -0.3855 -0.3662&nbsp; 0.2965 -0.1=
799 -0.2729&nbsp; 0.1466<br>&nbsp; Px&nbsp; C&nbsp; 1 -0.0710 -0.1061 -0.10=
44 -0.0410 -0.0398&nbsp; 0.0921&nbsp; 0.2435 -0.1648<br>&nbsp; Py&nbsp; C&n=
bsp; 1 -0.0125 -0.0125&nbsp; 0.0008&nbsp; 0.0230 -0.0359&nbsp; 0.0378 -0.07=
19&nbsp; 0.0727<br>=0A&nbsp; Pz&nbsp; C&nbsp; 1 -0.0016 -0.0004&nbsp; 0.002=
2&nbsp; 0.0022&nbsp; 0.0032 -0.0147&nbsp; 0.0045 -0.0002<br>&nbsp; S&nbsp;&=
nbsp; C&nbsp; 2 -0.2852 -0.3992 -0.3553 -0.1230 -0.0803&nbsp; 0.1349&nbsp; =
0.3741 -0.2315<br>&nbsp; Px&nbsp; C&nbsp; 2 -0.0130&nbsp; 0.0324&nbsp; 0.13=
00&nbsp; 0.2048 -0.1953&nbsp; 0.0878&nbsp; 0.1430 -0.0600<br>=0A&nbsp; Py&n=
bsp; C&nbsp; 2 -0.0619 -0.0591&nbsp; 0.0039&nbsp; 0.0897 -0.1163&nbsp; 0.08=
82 -0.1543&nbsp; 0.1498<br>.........<br>and&nbsp; Root No.&nbsp;&nbsp;&nbsp=
; 9&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 10&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 11&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp; 12&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp; 14&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp; 16<br><br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp; 9 A&nbsp;&nbsp;&nbsp; 10 A&nbsp;&nbsp;&nbsp; 11 A&nbsp=
;&nbsp;&nbsp; 12 A&nbsp;&nbsp;&nbsp; 13 A&nbsp;&nbsp;&nbsp; 14 A&nbsp;&nbsp=
;&nbsp; 15 A&nbsp;&nbsp;&nbsp; 16 A&nbsp;&nbsp; <br>=0A<br>&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -16.372 -15.825 -15.103 -14.91=
1 -14.409 -13.993 -13.166 -12.837<br>&nbsp; <br>&nbsp; S&nbsp;&nbsp; C&nbsp=
; 1&nbsp; 0.0584&nbsp; 0.0193 -0.0318 -0.0135 -0.0222 -0.0010 -0.0170&nbsp;=
 0.0373<br>&nbsp; Px&nbsp; C&nbsp; 1 -0.1888 -0.0755&nbsp; 0.3150&nbsp; 0.1=
065&nbsp; 0.2760 -0.1557 -0.1153&nbsp; 0.2238<br>=0A&nbsp; Py&nbsp; C&nbsp;=
 1 -0.2164&nbsp; 0.2561&nbsp; 0.2688 -0.0859 -0.2704&nbsp; 0.0105 -0.0940&n=
bsp; 0.0989<br>&nbsp; Pz&nbsp; C&nbsp; 1 -0.0448 -0.0097 -0.0142 -0.0804&nb=
sp; 0.0208&nbsp; 0.0267 -0.1218 -0.0939<br><br><br>=0A</div></blockquote></=
td></tr></table><br>=0A=0A      
--0-2092961422-1258820274=:21464--


From owner-chemistry@ccl.net Sat Nov 21 11:54:00 2009
From: "Mariusz Radon mariusz.radon[]gmail.com" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: Which program to optimize the crystal structure of transition metal complex?
Message-Id: <-40740-091121101537-4299-ofpkhNDYzxiXdESuqv+NBA=server.ccl.net>
X-Original-From: Mariusz Radon <mariusz.radon]~[gmail.com>
Content-Transfer-Encoding: quoted-printable
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Date: Sat, 21 Nov 2009 15:49:39 +0100
MIME-Version: 1.0


Sent to CCL by: Mariusz Radon [mariusz.radon^gmail.com]
> My propositions are Turbomole and Orca (...)

What I am looking for is a program being able to optimize the *crystal
structure* (solid state), not only a single molecule in vacuo (I know
that Turbomole and Orca master in it...).  In the other words: I would
like to optimize the molecules in the crystal and the parameters of
the unit cell, simultaneously. I don't think these features are really
implemented in Turbomole or Orca (or maybe I am wrong?)

My question is still open for your suggestions!

Best regards,
Mariusz Radon



On Sat, Nov 21, 2009 at 9:27 AM, Adam Kubas adam.kubas]*[kit.edu
<owner-chemistry^^^ccl.net> wrote:
>
> Sent to CCL by: Adam Kubas [adam.kubas^kit.edu]
> Dear Mariusz,
>
> My propositions are Turbomole and Orca - first is the fastest DFT code
> I've ever seen with wide range of options to control spin state of
> optimized compound but you have to buy it (free demo is available).
> The second program is a free package and is easily to use.
>
> 2009/11/20 Mariusz Radon mariusz.radon(0)gmail.com <owner-chemistry,,ccl.=
net>:
>>
>> Sent to CCL by: Mariusz Radon [mariusz.radon]-[gmail.com]
>> Dear Colleagues,
>>
>> I am looking for a program being able to optimize the crystal
>> structure of transition metal complex (molecular structure and unit
>> cell parameters) at DFT level. An important point is that I must be
>> able to control the spin state of the complex, because I would like to
>> perform such optimizations for different spin states in order to
>> capture the influence of the spin state on the molecular structure and
>> packing in the crystal.
>>
>> Could you recommend me any program capable to achieve this goal
>> (preferably, but not necessarily free software)? Thank you in advance
>> very much.
>>
>> Best regards,
>> Mariusz Radon
>
>
> --
> Adam Kubas
> Karlsruher Institut f=C3=BCr Technologie (KIT)
> Institut f=C3=BCr Physikalische Chemie
> Abteilung f=C3=BCr Theoretische Chemie
> Geb. 30.45, Kaiserstra=C3=9Fe 12, D-76131 Karlsruhe
> http://www.ipc.uni-karlsruhe.de/theochem/
> ----------------------------------------------------------------------
> Office:
> Institut f=C3=BCr Nanotechnologie
> Raum: 640/0-333
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Tel.: +49 7247 82-8834
> http://www.int.kit.edu
>
> KIT - Universit=C3=A4t des Landes Baden-W=C3=BCrttemberg und
> nationales Gro=C3=9Fforschungszentrum in der Helmholtz-Gemeinschaft
>
>
>
> - This is automatically added to each message by the mailing script -> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/chemistry/sub_unsub.shtml> =C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt>
>
>



--=20
Mariusz Radon, PhD student
Department of Theoretical Chemistry
Jagiellonian University
http://www.chemia.uj.edu.pl/~mradon
mradon /at/ chemia.uj.edu.pl
(PGP public key available on the website)


From owner-chemistry@ccl.net Sat Nov 21 12:30:01 2009
From: "William F. Coleman wcoleman##wellesley.edu" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: How can I find the HOMO from the MOPAC output??
Message-Id: <-40741-091121115122-17270-+gEolFXpKDC4Q7iroNOiTg _ server.ccl.net>
X-Original-From: "William F. Coleman" <wcoleman _ wellesley.edu>
Content-Type: multipart/alternative; boundary="--=_--1edd283c.1edd2747.c72dbf2b"
Date: Sat, 21 Nov 2009 11:00:43 -0500
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Sent to CCL by: "William F. Coleman" [wcoleman|a|wellesley.edu]
This is a multi-part message in MIME format.

----=_--1edd283c.1edd2747.c72dbf2b
Content-Type: text/plain; charset=UTF-8
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The orbitals are arranged in order of increasing energy.  You just need to
know how many electrons are in your system, and divide that number by two
to get the number of the HOMO.  It is not clear which method you used, but
the energies strike me as odd as all are negative.  Are these all of the
eigenvectors you obtained (I don't use MOPAC so am not exactly sure how
the output appears.

Cheers,

Flick


_______________
William F. Coleman
Professor of Chemistry
Wellesley College 
Wellesley MA 02481

www.wellesley.edu/Chemistry/colemanw.html

Editor, JCE WebWare and JCE Featured Molecules
http://www.jce.divched.org/JCEDLib/WebWare/
http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html



----=_--1edd283c.1edd2747.c72dbf2b
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<?xml version=3D=221.0=22 encoding=3D=22UTF-8=22?>
<=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
<html xmlns=3D=22http://www.w3.org/1999/xhtml=22>
<head>
<meta http-equiv=3D=22Content-Type=22 content=3D=22text/html; charset=3DUTF=
-8=22 />
<title></title>
<style type=3D=22text/css=22>
<=21--
body=7Bmargin-left:10px;margin-right:10px;margin-top:10px;margin-bottom:10p=
x;=7D
-->
</style>
</head>
<body marginleft=3D=2210=22 marginright=3D=2210=22 margintop=3D=2210=22 mar=
ginbottom=3D=2210=22>
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>The orbitals are arranged in order of=
 increasing energy. &nbsp;You just need to know how many electrons are in y=
our system, and divide that number by two to get the number of the HOMO. &n=
bsp;It is not clear which method you used, but the energies strike me as od=
d as all are negative. &nbsp;Are these all of the eigenvectors you obtained=
 (I don't use MOPAC so am not exactly sure how the output
appears.</font></div>
<br />
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>Cheers,</font></div>
<br />
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>Flick</font></div>
<br />
<br />
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>_______________</font></div>
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>William F. Coleman</font></div>
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>Professor of Chemistry</font></div>
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>Wellesley College </font></div>
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>Wellesley MA 02481</font></div>
<br />
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22><a href=3D=22http://www.wellesley.edu=
/Chemistry/colemanw.html=22 target=3D=22_blank=22>www.wellesley.edu/Chemist=
ry/colemanw.html</a></font></div>
<br />
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22>Editor, JCE WebWare and JCE Featured =
Molecules</font></div>
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22><a href=3D=22http://www.jce.divched.o=
rg/JCEDLib/WebWare/=22 target=3D=22_blank=22>http://www.jce.divched.org/JCE=
DLib/WebWare/</a></font></div>
<div align=3D=22left=22 style=3D=22text-align:left;=22><font face=3D=22Verd=
ana=22 size=3D=22+1=22 color=3D=22=230000DD=22 style=3D=22font-family:Verda=
na;font-size:14pt;color:=230000DD;=22><a href=3D=22http://jchemed.chem.wisc=
.edu/JCEWWW/Features/MonthlyMolecules/index.html=22 target=3D=22_blank=22>h=
ttp://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html</a>=
</font></div>
<br />
<br/>
</body>
</html>

----=_--1edd283c.1edd2747.c72dbf2b--


From owner-chemistry@ccl.net Sat Nov 21 14:02:00 2009
From: "John McKelvey jmmckel|a|gmail.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Which program to optimize the crystal structure of transition metal complex?
Message-Id: <-40742-091121084523-27234-DkToLcB/I+VVYZFo9dqjsA*server.ccl.net>
X-Original-From: John McKelvey <jmmckel#,#gmail.com>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=ISO-8859-1
Date: Sat, 21 Nov 2009 08:45:10 -0500
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel^gmail.com]
Folks,

Though a DFT method suggestion was requested for this, one might find
it interesting to consider looking at trends using the recent work of
Jimmy Stewart's PM6 in MOPAC 2009.  Itis extremely fast, has periodic
capabilities, and Jimmy has used it to model X-RAY structures.

Cheers,

John McKelvey

On 11/21/09, Adam Kubas adam.kubas]*[kit.edu <owner-chemistry-x-ccl.net> wrot=
e:
>
> Sent to CCL by: Adam Kubas [adam.kubas^kit.edu]
> Dear Mariusz,
>
> My propositions are Turbomole and Orca - first is the fastest DFT code
> I've ever seen with wide range of options to control spin state of
> optimized compound but you have to buy it (free demo is available).
> The second program is a free package and is easily to use.
>
> 2009/11/20 Mariusz Radon mariusz.radon(0)gmail.com
> <owner-chemistry,,ccl.net>:
>>
>> Sent to CCL by: Mariusz Radon [mariusz.radon]-[gmail.com]
>> Dear Colleagues,
>>
>> I am looking for a program being able to optimize the crystal
>> structure of transition metal complex (molecular structure and unit
>> cell parameters) at DFT level. An important point is that I must be
>> able to control the spin state of the complex, because I would like to
>> perform such optimizations for different spin states in order to
>> capture the influence of the spin state on the molecular structure and
>> packing in the crystal.
>>
>> Could you recommend me any program capable to achieve this goal
>> (preferably, but not necessarily free software)? Thank you in advance
>> very much.
>>
>> Best regards,
>> Mariusz Radon
>
>
> --
> Adam Kubas
> Karlsruher Institut f=FCr Technologie (KIT)
> Institut f=FCr Physikalische Chemie
> Abteilung f=FCr Theoretische Chemie
> Geb. 30.45, Kaiserstra=DFe 12, D-76131 Karlsruhe
> http://www.ipc.uni-karlsruhe.de/theochem/
> ----------------------------------------------------------------------
> Office:
> Institut f=FCr Nanotechnologie
> Raum: 640/0-333
> Hermann-von-Helmholtz-Platz 1
> 76344 Eggenstein-Leopoldshafen
> Tel.: +49 7247 82-8834
> http://www.int.kit.edu
>
> KIT - Universit=E4t des Landes Baden-W=FCrttemberg und
> nationales Gro=DFforschungszentrum in der Helmholtz-Gemeinschaft
>
>
>
> - This is automatically added to each message by the mailing script ->
>
>


--=20
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel-x-gmail.com


From owner-chemistry@ccl.net Sat Nov 21 22:16:01 2009
From: "qiancheng shen qianchengshen!A!gmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: How can I find the HOMO from the MOPAC output??
Message-Id: <-40743-091121221448-2834-FSqD4SAz9N5P78lY9Rgryg++server.ccl.net>
X-Original-From: qiancheng shen <qianchengshen^_^gmail.com>
Content-Type: multipart/alternative; boundary=0016364ee7cee37b850478ed1bdd
Date: Sun, 22 Nov 2009 11:14:37 +0800
MIME-Version: 1.0


Sent to CCL by: qiancheng shen [qianchengshen * gmail.com]
--0016364ee7cee37b850478ed1bdd
Content-Type: text/plain; charset=ISO-8859-1

Dear Morad,
        Thank you for your reply. It really works.

Best regards,
Qiancheng

2009/11/22 Morad El-Hendawy m80elhendawy*|*yahoo.com <
owner-chemistry+*+ccl.net>

> Dear Qiancheng,
> Go to Berif outpout, you will foind a summary like below:
>
> FINAL HEAT OF FORMATION = 26.97779 KCAL
> TOTAL ENERGY = -19.78933 EV
> ELECTRONIC ENERGY = -27.20810 EV
> CORE-CORE REPULSION = 7.41878 EV
> IONIZATION POTENTIAL = 8.38124
> NO. OF FILLED LEVELS = 1
> MOLECULAR WEIGHT = 7.948
>
> From the value of ionization potential you can specify the HOMO level;
> because the former is negative value of the later. See this representative
> example for LiH molecule:
>
> TOTAL ENERGY = -19.78933 EV
> ELECTRONIC ENERGY = -27.20810 EV
> CORE-CORE REPULSION = 7.41878 EV
> IONIZATION POTENTIAL = 8.38124
> NO. OF FILLED LEVELS = 1
> MOLECULAR WEIGHT = 7.948
> EIGENVECTORS
> ROOT NO. 1             2            3            4              5
>                 -8.38124  0.63258   2.45221   2.45221    5.60161
>
> S Li     1    0.41230   0.80110   0.00000  0.00000  -0.43387
> PX Li   1    0.34007   -0.57714  0.00000  0.00000  -0.74247
> PY Li   1    0.00000   0.00000  -0.92376  0.38298  0.00000
> PZ Li   1    0.00000   0.00000   0.38298  0.92376   0.00000
>
> Best regards
> *
> **************************************************************************************************
> *
> *Morad M. El-Hendawy*
> Ireland
> *
> **************************************************************************************************
> *
> ** *If you want a happy life, do four things:*
> **
> *1- Contemplate and be thankful,
> 2- The past is gone forever,
> 3- Today all that you have,
> 4- Leave the future alone until it come. *
> *
> *******************************************************************************************************************
> *
> **
>
> --- On *Sat, 11/21/09, qiancheng shen qianchengshen{:}gmail.com
> <owner-chemistry/a\ccl.net>* wrote:
>
>
> From: qiancheng shen qianchengshen{:}gmail.com <owner-chemistry/a\ccl.net>
> Subject: CCL: How can I find the HOMO from the MOPAC output??
> To: "El-Hendawy, Morad Metwally " <m80elhendawy/a\yahoo.com>
> Date: Saturday, November 21, 2009, 5:53 AM
>
> Dear CCLers,
>         I got a MOPAC output file will all EIGENVECTORS printed out. But,
> Which Molecular Orbital is the HOMO?
>         Could anyone help me?
>
>         The output MO information looks like:
>
>         Root No.    1       2       3       4       5       6       7
> 8
>
>               1 A     2 A     3 A     4 A     5 A     6 A     7 A     8 A
>
>
>            -37.523 -35.473 -32.665 -29.061 -25.420 -22.108 -20.717 -19.976
>
>   S   C  1 -0.1694 -0.2922 -0.3855 -0.3662  0.2965 -0.1799 -0.2729  0.1466
>   Px  C  1 -0.0710 -0.1061 -0.1044 -0.0410 -0.0398  0.0921  0.2435 -0.1648
>   Py  C  1 -0.0125 -0.0125  0.0008  0.0230 -0.0359  0.0378 -0.0719  0.0727
>   Pz  C  1 -0.0016 -0.0004  0.0022  0.0022  0.0032 -0.0147  0.0045 -0.0002
>   S   C  2 -0.2852 -0.3992 -0.3553 -0.1230 -0.0803  0.1349  0.3741 -0.2315
>   Px  C  2 -0.0130  0.0324  0.1300  0.2048 -0.1953  0.0878  0.1430 -0.0600
>   Py  C  2 -0.0619 -0.0591  0.0039  0.0897 -0.1163  0.0882 -0.1543  0.1498
> .........
> and  Root No.    9      10      11      12      13      14      15      16
>
>               9 A    10 A    11 A    12 A    13 A    14 A    15 A    16 A
>
>
>            -16.372 -15.825 -15.103 -14.911 -14.409 -13.993 -13.166 -12.837
>
>   S   C  1  0.0584  0.0193 -0.0318 -0.0135 -0.0222 -0.0010 -0.0170  0.0373
>   Px  C  1 -0.1888 -0.0755  0.3150  0.1065  0.2760 -0.1557 -0.1153  0.2238
>   Py  C  1 -0.2164  0.2561  0.2688 -0.0859 -0.2704  0.0105 -0.0940  0.0989
>   Pz  C  1 -0.0448 -0.0097 -0.0142 -0.0804  0.0208  0.0267 -0.1218 -0.0939
>
>
>
>

--0016364ee7cee37b850478ed1bdd
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Morad,<br>=A0=A0=A0=A0=A0=A0=A0 Thank you for your reply. It really wo=
rks.<br><br>Best regards,<br>Qiancheng<br><br><div class=3D"gmail_quote">20=
09/11/22 Morad El-Hendawy m80elhendawy*|*<a href=3D"http://yahoo.com">yahoo=
.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry+*+ccl.net">o=
wner-chemistry+*+ccl.net</a>&gt;</span><br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border=3D"=
0" cellpadding=3D"0" cellspacing=3D"0"><tbody><tr><td style=3D"font-family:=
 inherit; font-style: inherit; font-variant: inherit; font-weight: inherit;=
 font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-=
stretch: inherit;" valign=3D"top">
Dear Qiancheng,<br>Go to Berif outpout, you will foind a summary like below=
: <br><br>FINAL HEAT OF FORMATION =3D 26.97779 KCAL<br>TOTAL ENERGY =3D -19=
.78933 EV<br>ELECTRONIC ENERGY =3D -27.20810 EV<br>CORE-CORE REPULSION =3D =
7.41878 EV<br>
IONIZATION POTENTIAL =3D 8.38124<br>NO. OF FILLED LEVELS =3D 1<br>MOLECULAR=
 WEIGHT =3D 7.948<br><br>From the value of ionization potential you can spe=
cify the HOMO level; because the former is negative value of the later. See=
 this representative example for LiH molecule:<br>
<br>TOTAL ENERGY =3D -19.78933 EV<br>ELECTRONIC ENERGY =3D -27.20810 EV<br>=
CORE-CORE REPULSION =3D 7.41878 EV<br>IONIZATION POTENTIAL =3D <span style=
=3D"background-color: rgb(255, 255, 0);">8.38124</span><br>NO. OF FILLED LE=
VELS =3D 1<br>
MOLECULAR WEIGHT =3D 7.948<br>EIGENVECTORS<br>ROOT NO. 1=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0
 2=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 3=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 4=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 5<br>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0<span style=3D"background-color: rgb(255, 255, 0);"> -8.38124</=
span>=A0 0.63258=A0=A0 2.45221=A0=A0 2.45221 =A0=A0 5.60161<br><br>S Li=A0=
=A0=A0=A0 1=A0=A0=A0 0.41230=A0=A0 0.80110=A0=A0 0.00000=A0 0.00000=A0 -0.4=
3387<br>
PX Li=A0=A0 1 =A0=A0 0.34007 =A0 -0.57714=A0 0.00000=A0 0.00000=A0 -0.74247=
<br>PY Li =A0 1 =A0=A0 0.00000=A0=A0 0.00000=A0 -0.92376=A0 0.38298=A0 0.00=
000<br>PZ Li=A0=A0 1 =A0=A0 0.00000=A0=A0 0.00000=A0=A0 0.38298=A0 0.92376=
=A0=A0 0.00000<br><br><div>Best regards<br><b><font color=3D"#00407f"><font=
 style=3D"background-color: rgb(230, 230, 230);" size=3D"4" face=3D"arial, =
helvetica, sans-serif">****************************************************=
**********************************************</font></font></b></div>
<div><b><font color=3D"#00407f"><font style=3D"background-color: rgb(230, 2=
30, 230);" face=3D"arial, helvetica, sans-serif">Morad M. El-Hendawy</font>=
</font></b></div><span style=3D"text-decoration: underline;"><span style=3D=
"font-weight: bold;">Ireland</span></span><br>
<div><b><font style=3D"background-color: rgb(230, 230, 230);" size=3D"4" co=
lor=3D"#00407f" face=3D"Arial">********************************************=
******************************************************</font></b></div><div=
><b><font style=3D"background-color: rgb(230, 230, 230);" color=3D"#00407f"=
></font></b><font size=3D"4">=A0</font><b><font style=3D"background-color: =
rgb(255, 128, 255);" size=3D"4" color=3D"#000000" face=3D"arial, helvetica,
 sans-serif">If you want a happy life, do four things:</font></b></div><div=
><b><font color=3D"#00407f"><font style=3D"background-color: rgb(230, 230, =
230);"></font></font></b><font size=3D"4" face=3D"arial, helvetica, sans-se=
rif">=A0</font></div>
<div><b><font color=3D"#00407f"><font style=3D"background-color: rgb(230, 2=
30, 230);" color=3D"#373e68" face=3D"arial, helvetica, sans-serif">1- Conte=
mplate and be thankful,<br></font><font face=3D"arial, helvetica, sans-seri=
f"><font style=3D"background-color: rgb(230, 230, 230);"><font color=3D"#37=
3e68">2- The past is gone forever,<br>
3- Today all that you have,<br>4- Leave the future alone until it come.</fo=
nt>=A0</font></font></font></b></div><div><b><font style=3D"background-colo=
r: rgb(230, 230, 230);" color=3D"#00407f" face=3D"Arial">******************=
***************************************************************************=
**********************</font></b></div>
<img src=3D"" alt=3D""><b></b><br><br>--- On <b>Sat, 11/21/09, qiancheng sh=
en qianchengshen{:}<a href=3D"http://gmail.com" target=3D"_blank">gmail.com=
</a> <i>&lt;owner-chemistry/a\<a href=3D"http://ccl.net" target=3D"_blank">=
ccl.net</a>&gt;</i></b> wrote:<br>
<blockquote style=3D"border-left: 2px solid rgb(16, 16, 255); margin-left: =
5px; padding-left: 5px;"><br>From: qiancheng shen qianchengshen{:}<a href=
=3D"http://gmail.com" target=3D"_blank">gmail.com</a> &lt;owner-chemistry/a=
\<a href=3D"http://ccl.net" target=3D"_blank">ccl.net</a>&gt;<br>
Subject: CCL: How can I find the HOMO from the MOPAC output??<br>To: &quot;=
El-Hendawy, Morad Metwally &quot; &lt;m80elhendawy/a\<a href=3D"http://yaho=
o.com" target=3D"_blank">yahoo.com</a>&gt;<br>Date: Saturday, November 21, =
2009, 5:53 AM<br>
<br><div>Dear CCLers,<br>=A0=A0=A0=A0=A0=A0=A0 I got a MOPAC output file wi=
ll all EIGENVECTORS printed out. But, Which Molecular Orbital is the HOMO?<=
br>=A0=A0=A0=A0=A0=A0=A0 Could anyone help me? <br><br>=A0=A0=A0=A0=A0=A0=
=A0 The output MO information looks like:<br>
=A0=A0=A0=A0=A0=A0=A0=A0 <br>
=A0=A0=A0=A0=A0=A0=A0 Root No.=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 2=A0=A0=A0=A0=
=A0=A0 3=A0=A0=A0=A0=A0=A0 4=A0=A0=A0=A0=A0=A0 5=A0=A0=A0=A0=A0=A0 6=A0=A0=
=A0=A0=A0=A0 7=A0=A0=A0=A0=A0=A0 8<br><br>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0 1 A=A0=A0=A0=A0 2 A=A0=A0=A0=A0 3 A=A0=A0=A0=A0 4 A=A0=A0=A0=A0 5 A=
=A0=A0=A0=A0 6 A=A0=A0=A0=A0 7 A=A0=A0=A0=A0 8 A=A0=A0 <br><br>=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0 -37.523 -35.473 -32.665 -29.061 -25.420 -22.108 -20.717 =
-19.976<br>

=A0 <br>=A0 S=A0=A0 C=A0 1 -0.1694 -0.2922 -0.3855 -0.3662=A0 0.2965 -0.179=
9 -0.2729=A0 0.1466<br>=A0 Px=A0 C=A0 1 -0.0710 -0.1061 -0.1044 -0.0410 -0.=
0398=A0 0.0921=A0 0.2435 -0.1648<br>=A0 Py=A0 C=A0 1 -0.0125 -0.0125=A0 0.0=
008=A0 0.0230 -0.0359=A0 0.0378 -0.0719=A0 0.0727<br>

=A0 Pz=A0 C=A0 1 -0.0016 -0.0004=A0 0.0022=A0 0.0022=A0 0.0032 -0.0147=A0 0=
.0045 -0.0002<br>=A0 S=A0=A0 C=A0 2 -0.2852 -0.3992 -0.3553 -0.1230 -0.0803=
=A0 0.1349=A0 0.3741 -0.2315<br>=A0 Px=A0 C=A0 2 -0.0130=A0 0.0324=A0 0.130=
0=A0 0.2048 -0.1953=A0 0.0878=A0 0.1430 -0.0600<br>

=A0 Py=A0 C=A0 2 -0.0619 -0.0591=A0 0.0039=A0 0.0897 -0.1163=A0 0.0882 -0.1=
543=A0 0.1498<br>.........<br>and=A0 Root No.=A0=A0=A0 9=A0=A0=A0=A0=A0 10=
=A0=A0=A0=A0=A0 11=A0=A0=A0=A0=A0 12=A0=A0=A0=A0=A0 13=A0=A0=A0=A0=A0 14=A0=
=A0=A0=A0=A0 15=A0=A0=A0=A0=A0 16<br><br>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0 9 A=A0=A0=A0 10 A=A0=A0=A0 11 A=A0=A0=A0 12 A=A0=A0=A0 13 A=A0=A0=A0=
 14 A=A0=A0=A0 15 A=A0=A0=A0 16 A=A0=A0 <br>

<br>=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 -16.372 -15.825 -15.103 -14.911 -14.409 =
-13.993 -13.166 -12.837<br>=A0 <br>=A0 S=A0=A0 C=A0 1=A0 0.0584=A0 0.0193 -=
0.0318 -0.0135 -0.0222 -0.0010 -0.0170=A0 0.0373<br>=A0 Px=A0 C=A0 1 -0.188=
8 -0.0755=A0 0.3150=A0 0.1065=A0 0.2760 -0.1557 -0.1153=A0 0.2238<br>

=A0 Py=A0 C=A0 1 -0.2164=A0 0.2561=A0 0.2688 -0.0859 -0.2704=A0 0.0105 -0.0=
940=A0 0.0989<br>=A0 Pz=A0 C=A0 1 -0.0448 -0.0097 -0.0142 -0.0804=A0 0.0208=
=A0 0.0267 -0.1218 -0.0939<br><br><br>
</div></blockquote></td></tr></tbody></table><br>

      </blockquote></div><br>

--0016364ee7cee37b850478ed1bdd--


From owner-chemistry@ccl.net Sat Nov 21 22:59:00 2009
From: "Tobias Kind tkind/a\ucdavis.edu" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: chemoinformatics / a nomenclature challenge
Message-Id: <-40744-091120203520-7778-nahKVnt8BIuUngbHtCQGCQ+/-server.ccl.net>
X-Original-From: "Tobias Kind" <tkind.+/-.ucdavis.edu>
Date: Fri, 20 Nov 2009 15:23:15 -0800 (PST)


Sent to CCL by: "Tobias Kind" [tkind]|[ucdavis.edu]


Hello Michel,
actually the name was already posted back in 2006 and 2009.
1) sci.tech-archive.net/Archive/sci.chem/2006-06/msg00154.html
2) darkhammer.multiply.com/journal/item/223

Marvin from ChemAxon can import and export the correct name.
Hence it can create the name from the connection table, and it can create
the molecule connection table from the name. I don't know if the IUPAC Name
is correct (I guess so, maybe Daniel the author can help) but at least its
consistent within the algorithm. Regarding the generation of all
stereoisomers and the correct naming of those molecules, that is a
different case I would say and unless somebody cooks that molecule also of
lesser importance than lets say the pig flu. 

Run Marvin free with JAVA (Naming is licensed):
http://www.chemaxon.com/marvin/examples/webstart/mview.jnlp

[6.6]chiralane
tetradecacyclo[13.11.1.0^{1,18}.0^{2,7}.0^{2,11}.0^{3,14}.0^{5,27}.0^{6,25}.0^{9,26}.0^{10,19}.0^{13,18}.0^{17,22}.0^{21,26}.0^{23,27}]heptacosane

[6.6]chiralane
InChI=1S/C27H28/c1-7-19-9-2-15-21-13-5-12-20-8(1)23(9,13)27-24(7)10(20)3-16-22-14(24)4-11(19)25(15,27)18(22)6-17(21)26(12,16)27/h7-22H,1-6H2

[6.6]chiralane InChIKey JKJBBXWDXQSMMM-OXSFYKJQBU

http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html#CHIR
If I wouldn't know better I would say that looks like a typical Uncle Al
question, well it was :-)

Cheers
Tobias Kind
http://fiehnlab.ucdavis.edu/



> Sent to CCL by: Michel Petitjean [petitjean.chiral%x%gmail.com]
> Dear CCLers,
> 
> Here is my challenge: assign a name to the [6.6]chiralane, C27H28.
> The connection table is available from
> http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html#CHIR
> If somebody has a programme running successfully on this small molecule,
> please tell me and send me the name:
> until now, nomenclature assignment programmes failed !
> Furthermore, I would be delighted to know what name is
> generated from CAS or IUPAC rules.
> Many thanks.
> 
> All my best,
> 
> Michel Petitjean,
> CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096),
> 91191 Gif-sur-Yvette Cedex, France.
> Phone: +331 6908 4006 / Fax: +331 6908 4007
> E-mail: michel.petitjean,,cea.fr, petitjean.chiral,,gmail.com (preferred)
> http://petitjeanmichel.free.fr/itoweb.petitjean.html> 
> 
> 

Dr. Tobias Kind
UC Davis Genome Center
Metabolomics Group

http://genomecenter.ucdavis.edu
Tel:+1-530-752-9922