From owner-chemistry@ccl.net Thu Jan 20 00:49:01 2011
From: "prakash surya tarzan11_11^yahoo.com" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: spin contamination
Message-Id: <-43704-110119084704-22099-dcq7qtr4HNCDMTlX8iFxLA|*|server.ccl.net>
X-Original-From: "prakash surya" <tarzan11_11]=[yahoo.com>
Date: Wed, 19 Jan 2011 08:47:01 -0500
Sent to CCL by: "prakash surya" [tarzan11_11^-^yahoo.com]
Hi all
a small doubt.
The wavefunction obtained as a slater determinant under UHF is essentially not
a eigen function of the spin operator s^2. so, higher the value of the <s^2>,
it signifies the mixing of higher exited states contributed by higher spin
states and the wave functions has lesser physical significance. right ...!!!
so my question is how much of <s^2> is OK , since during my gaussuian
calcualtions i some times observe a <s^2> as much as 2.0
thanx in advance
pls let me know if i am wrong any way ..:)
email: tarzan11_11^yahoo.com
From owner-chemistry@ccl.net Thu Jan 20 01:44:00 2011
From: "Georg Lefkidis lefkidis++physik.uni-kl.de" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: spin contamination
Message-Id: <-43705-110120014042-21599-VbpTwCKsLUDflnEjpc8CtA(-)server.ccl.net>
X-Original-From: "Georg Lefkidis" <lefkidis|,|physik.uni-kl.de>
Content-Transfer-Encoding: 7bit
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Date: Thu, 20 Jan 2011 07:40:15 +0100
Mime-Version: 1.0
Sent to CCL by: "Georg Lefkidis" [lefkidis a physik.uni-kl.de]
Dear Prakash,
the problem of the UHF is that it still neglects correlations. That means
that when virtual excitations are included you will most probably get a
wavefunction with lower energy for a clear cut expectation value of <s^2>.
UHF tends to increase <s^2> because it considers not "completely paired"
electrons. However even more unpaired electrons when treated in a CI way can
give lower multiplicities than the maximum possible. So you can obtain a
singlet with two unpaired electrons \frac{(|ab>-|ba>)}{\sqrt{2}}, and this
cannot be found with a single-determinant method like RHF, ROHF or UHF.
Therefore high spin contamination can be an indication, but is to be treated
with caution. A typical example is a molecule with antiferromagnetic
coupling.
It is always better to check it with an adequate method before making a
statement. Besides the more unpaired electrons the more possible that UHF
will converge to a high multiplicity value. For triplets a value of <s^2>
around 2 is a strong indication, but a value of 2.5 still does not mean much
if not checked with a CI (or CI-derivative) method.
Cheers
George
prakash surya tarzan11_11^yahoo.com writes:
>
> Sent to CCL by: "prakash surya" [tarzan11_11^-^yahoo.com]
> Hi all
> a small doubt.
> The wavefunction obtained as a slater determinant under UHF is essentially not
> a eigen function of the spin operator s^2. so, higher the value of the <s^2>,
> it signifies the mixing of higher exited states contributed by higher spin
> states and the wave functions has lesser physical significance. right ...!!!
> so my question is how much of <s^2> is OK , since during my gaussuian
> calcualtions i some times observe a <s^2> as much as 2.0
>
> thanx in advance
> pls let me know if i am wrong any way ..:)
> email: tarzan11_11_._yahoo.com>
>
---------------------------------------------------------------
Dr. Georg Lefkidis
E-mail:lefkidis(at)physik(dot)uni(dash)kl(dot)de University of
Kaiserslautern
Tel. +49 631 205 3207 Department of Physics
Fax: +49 631 205 3907 PO Box 3049
67653 Kaiserslautern
Germany
---------------------------------------------------------------
From owner-chemistry@ccl.net Thu Jan 20 02:18:00 2011
From: "Marcel Swart marcel.swart-,-icrea.cat" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: spin contamination
Message-Id: <-43706-110120015444-3314-c0o4bspbQILXG1NVgrx67g~!~server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart|a|icrea.cat>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=iso-8859-1
Date: Thu, 20 Jan 2011 07:54:48 +0100
Mime-Version: 1.0 (Apple Message framework v1082)
Sent to CCL by: Marcel Swart [marcel.swart-.-icrea.cat]
A value of 2.0 is perfect, if you're studying a triplet.
If not, then you have a serious problem.
M.
On 19 Jan 2011, at 14:47, prakash surya tarzan11_11^yahoo.com wrote:
> Sent to CCL by: "prakash surya" [tarzan11_11^-^yahoo.com]
> Hi all
> a small doubt.
> The wavefunction obtained as a slater determinant under UHF is essentially not
> a eigen function of the spin operator s^2. so, higher the value of the <s^2>,
> it signifies the mixing of higher exited states contributed by higher spin
> states and the wave functions has lesser physical significance. right ...!!!
> so my question is how much of <s^2> is OK , since during my gaussuian
> calcualtions i some times observe a <s^2> as much as 2.0
>
> thanx in advance
> pls let me know if i am wrong any way ..:)
> email: tarzan11_11_._yahoo.com
===================================
dr. Marcel Swart
ICREA Research Professor at
Institut de Qu�mica Computacional
Universitat de Girona
Facultat de Ci�ncies
Campus Montilivi
17071 Girona
Catalunya (Spain)
tel
+34-972-418861
fax
+34-972-418356
e-mail
marcel.swart:-:icrea.cat
marcel.swart:-:udg.edu
web
http://www.marcelswart.eu
===================================
From owner-chemistry@ccl.net Thu Jan 20 05:53:00 2011
From: "Lukman Olawale Olasunkanmi waleolasunkanmi : gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: Help on articles
Message-Id: <-43707-110120053354-30684-z3lSiQOT11UlH+jNO7t6RA,+,server.ccl.net>
X-Original-From: Lukman Olawale Olasunkanmi <waleolasunkanmi() gmail.com>
Content-Type: multipart/alternative; boundary=0016e65a073ec597fb049a44aa3a
Date: Thu, 20 Jan 2011 10:33:40 +0000
MIME-Version: 1.0
Sent to CCL by: Lukman Olawale Olasunkanmi [waleolasunkanmi(~)gmail.com]
--0016e65a073ec597fb049a44aa3a
Content-Type: text/plain; charset=ISO-8859-1
Dear All,
I need some reference data as benchmarks for my results.
Does any one know of articles where I can get data like: Heat of formation,
enthalpy, entropy, free energy, HOMO-LUMO energies, Ionization potential,
Dipole moment etc. of phenanthroline and its metal complexes (Fe2+, Pt2+,
Ni2+ etc.), preferably computed with semi empirical methods (AM1, PM3 etc.).
Experimental or data from any other computational methods would also be
okay.
thank you in anticipation.
--
Olasunkanmi Lukman Olawale
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Nigeria.
+234-08052401564
--0016e65a073ec597fb049a44aa3a
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Dear All,<br>I need some reference data as benchmarks for my results.<br>Do=
es any one know of articles where I can get data like: Heat of formation, e=
nthalpy, entropy, free energy, HOMO-LUMO energies, Ionization potential, Di=
pole moment etc. of phenanthroline and its metal complexes (Fe2+, Pt2+, Ni2=
+ etc.), preferably computed with semi empirical methods (AM1, PM3 etc.). E=
xperimental or data from any other computational methods would also be okay=
.<br>
thank you in anticipation.<br clear=3D"all"><br>-- <br>Olasunkanmi Lukman O=
lawale<br>Department of Chemistry,<br>Obafemi Awolowo University,<br>Ile-If=
e, Nigeria.<br>+234-08052401564<br>
--0016e65a073ec597fb049a44aa3a--
From owner-chemistry@ccl.net Thu Jan 20 06:59:00 2011
From: "Bruce Palfey brupalf a umich.edu" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: Help on articles
Message-Id: <-43708-110120065640-12524-QEOs90hWdjt8G9H28b8s0w::server.ccl.net>
X-Original-From: Bruce Palfey <brupalf[-]umich.edu>
Content-Type: multipart/alternative; boundary=Apple-Mail-183--610204452
Date: Thu, 20 Jan 2011 06:56:15 -0500
Mime-Version: 1.0 (Apple Message framework v1082)
Sent to CCL by: Bruce Palfey [brupalf- -umich.edu]
--Apple-Mail-183--610204452
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
charset=us-ascii
Experimental thermodynamic data for the formation of many complexes can =
be found in: Christensen, J. J., Hansen, L. D., & Izatt, R. M. (1983) =
"Handbook of Metal Ligand Heats and Related Thermodynamic Quantities", =
Marcel Dekker, NY.
ciao,
Bruce
Bruce A. Palfey
Associate Professor &
Associate Director, Chemical Biology Ph.D. Program
Department of Biological Chemistry
University of Michigan Medical School
5220E MSRB III
1150 W. Medical Center Drive
Ann Arbor, MI 48109-5606
(734) 615-2452
brupalf!=!umich.edu
http://www.biochem.med.umich.edu/?q=3Dpalfey
http://www.chembio.umich.edu/people/palfey.html
On Jan 20, 2011, at 5:33 AM, Lukman Olawale Olasunkanmi waleolasunkanmi =
: gmail.com wrote:
> Dear All,
> I need some reference data as benchmarks for my results.
> Does any one know of articles where I can get data like: Heat of =
formation, enthalpy, entropy, free energy, HOMO-LUMO energies, =
Ionization potential, Dipole moment etc. of phenanthroline and its metal =
complexes (Fe2+, Pt2+, Ni2+ etc.), preferably computed with semi =
empirical methods (AM1, PM3 etc.). Experimental or data from any other =
computational methods would also be okay.
> thank you in anticipation.
>=20
> --=20
> Olasunkanmi Lukman Olawale
> Department of Chemistry,
> Obafemi Awolowo University,
> Ile-Ife, Nigeria.
> +234-08052401564
--Apple-Mail-183--610204452
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
charset=us-ascii
<html><head></head><body style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; =
">Experimental thermodynamic data for the formation of many complexes =
can be found in: Christensen, J.
J., Hansen, L. D., & Izatt, R. M. (1983) "Handbook of Metal Ligand
Heats and Related Thermodynamic Quantities", Marcel Dekker, =
NY.<!--StartFragment--><!--EndFragment--><div><br></div><div>ciao,</div><d=
iv>Bruce</div><div><br></div><div><div><div style=3D"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; "><span class=3D"Apple-style-span" =
style=3D"border-collapse: separate; color: rgb(0, 0, 0); font-family: =
Helvetica; font-size: 12px; font-style: normal; font-variant: normal; =
font-weight: normal; letter-spacing: normal; line-height: normal; =
orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; =
widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; =
-webkit-border-vertical-spacing: 0px; =
-webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: =
auto; -webkit-text-stroke-width: 0px; "><div style=3D"word-wrap: =
break-word; -webkit-nbsp-mode: space; -webkit-line-break: =
after-white-space; "><div>Bruce A. Palfey<br>Associate Professor =
&<br>Associate Director, Chemical Biology Ph.D. =
Program<br>Department of Biological Chemistry<br>University of Michigan =
Medical School<br>5220E MSRB III<br>1150 W. Medical Center Drive<br>Ann =
Arbor, MI 48109-5606<br>(734) 615-2452<br><a =
href=3D"mailto:brupalf!=!umich.edu">brupalf!=!umich.edu</a><br><br><a =
href=3D"http://www.biochem.med.umich.edu/?q=3Dpalfey">http://www.biochem.m=
ed.umich.edu/?q=3Dpalfey</a><br><a =
href=3D"http://www.chembio.umich.edu/people/palfey.html">http://www.chembi=
o.umich.edu/people/palfey.html</a><br></div><div><br></div></div></span></=
div></div></div><div><br></div><div><br></div><div><br><div><div>On Jan =
20, 2011, at 5:33 AM, Lukman Olawale Olasunkanmi waleolasunkanmi : <a =
href=3D"http://gmail.com">gmail.com</a> wrote:</div><br =
class=3D"Apple-interchange-newline"><blockquote type=3D"cite">Dear =
All,<br>I need some reference data as benchmarks for my results.<br>Does =
any one know of articles where I can get data like: Heat of formation, =
enthalpy, entropy, free energy, HOMO-LUMO energies, Ionization =
potential, Dipole moment etc. of phenanthroline and its metal complexes =
(Fe2+, Pt2+, Ni2+ etc.), preferably computed with semi empirical methods =
(AM1, PM3 etc.). Experimental or data from any other computational =
methods would also be okay.<br>
thank you in anticipation.<br clear=3D"all"><br>-- <br>Olasunkanmi =
Lukman Olawale<br>Department of Chemistry,<br>Obafemi Awolowo =
University,<br>Ile-Ife, Nigeria.<br>+234-08052401564<br>
</blockquote></div><br></div></body></html>=
--Apple-Mail-183--610204452--
From owner-chemistry@ccl.net Thu Jan 20 11:54:00 2011
From: "Dennis Sprous dsprous=-=redpointbio.com" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: InChi converters
Message-Id: <-43709-110120115241-2765-Xz6VXRcPom54T6vxWSY95g^^^server.ccl.net>
X-Original-From: "Dennis Sprous" <dsprous*redpointbio.com>
Date: Thu, 20 Jan 2011 11:52:39 -0500
Sent to CCL by: "Dennis Sprous" [dsprous()redpointbio.com]
Dear All:
I am interested in experiences with InChi to SDF or InChi to SMILES programs. I am using OpenBabel 2.3.0 which is doing OK. I am just wondering if there are other utilities out there.
-- Den
From owner-chemistry@ccl.net Thu Jan 20 13:24:01 2011
From: "Cheri Ann McFerrin cmcfer1..lsu.edu" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: lanl2dz basis set: GAMESS vs G09
Message-Id: <-43710-110120132240-5844-WHMdOwdiAMMuaDJQp+4Mzg#,#server.ccl.net>
X-Original-From: "Cheri Ann McFerrin" <cmcfer1|,|lsu.edu>
Date: Thu, 20 Jan 2011 13:22:38 -0500
Sent to CCL by: "Cheri Ann McFerrin" [cmcfer1{:}lsu.edu]
Hi Everyone:
The Lanl2dz basis for Copper at the EMSL basis set exchange (pnl.gov) in GAMESS-US format versus
the Lanl2dz basis for Copper using G09 are different. I am copying the coefficients & exponents
here for convenience, separated by asterisks. Can anyone tell me why the Lanl2dz basis is not
consistent with respect to GAMESS & G09? We are getting different equilibrium geometries and
eneriges as a result.
Thank you!!
Dr. Cheri McFerrin, LSU Dept of Chemistry, Baton Rouge, LA USA
***********************************************************************************
! LANL2DZ ECP EMSL Basis Set Exchange Library 1/20/11 10:05 AM
! Elements References
! -------- ----------
! H - Ne: T. H. Dunning Jr. and P. J. Hay, in Methods of Electronic Structure
! Theory, Vol. 2, H. F. Schaefer III, ed., PLENUM PRESS (1977)
! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985).
$DATA
COPPER
S 3
1 8.1760000 -0.4210260
2 2.5680000 0.7385924
3 0.9587000 0.5525692
S 4
1 8.1760000 0.1787665
2 2.5680000 -0.3592273
3 0.9587000 -0.4704825
4 0.1153000 1.0807407
S 1
1 0.0396000 1.0000000
P 3
1 25.6300000 -0.0489173
2 3.1660000 0.6272854
3 1.0230000 0.4716188
P 1
1 0.0860000 1.0000000
P 1
1 0.0240000 1.0000000
D 4
1 41.3400000 0.0465424
2 11.4200000 0.2227824
3 3.8390000 0.4539059
4 1.2300000 0.5314769
D 1
1 0.3102000 1.0000000
$END
! Elements References
! -------- ----------
! Na - Hg: P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 284 (1985).
! P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 299 (1985).
$ECP
CU-ECP GEN 10 2
3 ----- d potential -----
-10.0000000 1 511.9951763
-72.5548282 2 93.2801074
-12.7450231 2 23.2206669
4 ----- s-d potential -----
3.0000000 0 173.1180854
23.8351825 1 185.2419886
473.8930488 2 73.1517847
157.6345823 2 14.6884157
4 ----- p-d potential -----
5.0000000 0 100.7191369
6.4990936 1 130.8345665
351.4605395 2 53.8683720
85.5016036 2 14.0989469
$END
*********************from G09 output after using lanl2dz 6d*********************************
S 3 1.00 0.000000000000
0.2568000000D+01 -0.4632439327D-01
0.9587000000D+00 -0.2394893745D+00
0.1153000000D+00 0.1097356778D+01
S 3 1.00 0.000000000000
0.8176000000D+01 -0.4210259893D+00
0.2568000000D+01 0.7385923813D+00
0.9587000000D+00 0.5525691860D+00
S 1 1.00 0.000000000000
0.3960000000D-01 0.1000000000D+01
P 3 1.00 0.000000000000
0.2563000000D+02 -0.4891730019D-01
0.3166000000D+01 0.6272854025D+00
0.1023000000D+01 0.4716188019D+00
P 1 1.00 0.000000000000
0.8600000000D-01 0.1000000000D+01
P 1 1.00 0.000000000000
0.2400000000D-01 0.1000000000D+01
D 4 1.00 0.000000000000
0.4134000000D+02 0.4654240160D-01
0.1142000000D+02 0.2227824077D+00
0.3839000000D+01 0.4539059156D+00
0.1230000000D+01 0.5314769183D+00
D 1 1.00 0.000000000000
0.3102000000D+00 0.1000000000D+01
**************************************************************
From owner-chemistry@ccl.net Thu Jan 20 13:59:00 2011
From: "Wolf Ihlenfeldt wdi : xemistry.com" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: InChi converters
Message-Id: <-43711-110120133622-15983-vbH2zZ0RnbzORZ4KPmbKtg^-^server.ccl.net>
X-Original-From: Wolf Ihlenfeldt <wdi=xemistry.com>
Content-Type: multipart/alternative; boundary=001636c5a85ef96fe9049a4b64ea
Date: Thu, 20 Jan 2011 19:35:14 +0100
MIME-Version: 1.0
Sent to CCL by: Wolf Ihlenfeldt [wdi%a%xemistry.com]
--001636c5a85ef96fe9049a4b64ea
Content-Type: text/plain; charset=UTF-8
The CACTVS toolkit (www.xemistry.com) has full support for computing and
decoding InChI strings (with or without AuxInfo) and InChIKeys (both
old-style and new-style). For SDF, this includes capabilities to produce
nice 2D layouts (critical for stereochemistry) which in our opinion are
clearly superior to Babel output.
For commercial customers, there is also a turn-key converter application
which includes full InChI I/O support, plus support for many formats which
are not supported by Babel.
On Thu, Jan 20, 2011 at 5:52 PM, Dennis Sprous dsprous=-=redpointbio.com <
owner-chemistry_-_ccl.net> wrote:
>
> Sent to CCL by: "Dennis Sprous" [dsprous()redpointbio.com]
>
> Dear All:
>
> I am interested in experiences with InChi to SDF or InChi to SMILES
> programs. I am using OpenBabel 2.3.0 which is doing OK. I am just
> wondering if there are other utilities out there.
>
> -- Den>
>
>
--
Wolf-D. Ihlenfeldt, Xemistry GmbH
www.xemistry.com
--001636c5a85ef96fe9049a4b64ea
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable
The CACTVS toolkit (<a href=3D"http://www.xemistry.com">www.xemistry.com</a=
>) has full support for computing and decoding InChI strings (with or witho=
ut AuxInfo) and InChIKeys (both old-style and new-style). For SDF, this inc=
ludes capabilities to produce nice 2D layouts (critical for stereochemistry=
) which in our opinion are clearly superior to Babel output.<br>
<br>For commercial customers, there is also a turn-key converter applicatio=
n which includes full InChI I/O=C2=A0 support, plus support for many format=
s which are not supported by Babel.<br><br><br><div class=3D"gmail_quote">O=
n Thu, Jan 20, 2011 at 5:52 PM, Dennis Sprous dsprous=3D-=3D<a href=3D"http=
://redpointbio.com">redpointbio.com</a> <span dir=3D"ltr"><<a href=3D"ma=
ilto:owner-chemistry_-_ccl.net">owner-chemistry_-_ccl.net</a>></span> wrote:=
<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: "Dennis =C2=A0Sprous" [dsprous()<a href=3D"http:/=
/redpointbio.com" target=3D"_blank">redpointbio.com</a>]<br>
<br>
Dear All:<br>
<br>
I am interested in experiences with InChi to SDF or InChi to SMILES program=
s. =C2=A0I am using OpenBabel 2.3.0 which is doing OK. =C2=A0I am just wond=
ering if there are other utilities out there.<br>
<br>
-- Den<br>
<br>
<br>
<br>
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</blockquote></div><br><br clear=3D"all"><br>-- <br>Wolf-D. Ihlenfeldt, Xem=
istry GmbH<br><a href=3D"http://www.xemistry.com" target=3D"_blank">www.xem=
istry.com</a><br><br>
--001636c5a85ef96fe9049a4b64ea--
From owner-chemistry@ccl.net Thu Jan 20 17:23:01 2011
From: "Jason D Acchioli jdacchio---gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian on Centos?
Message-Id: <-43712-110120145308-23018-qS6plcWYF8QzBj+JNls9iw#,#server.ccl.net>
X-Original-From: "Jason D'Acchioli" <jdacchio{:}gmail.com>
Content-Type: multipart/alternative; boundary=00163630f5375a2c29049a4c79c9
Date: Thu, 20 Jan 2011 13:52:30 -0600
MIME-Version: 1.0
Sent to CCL by: "Jason D'Acchioli" [jdacchio+*+gmail.com]
--00163630f5375a2c29049a4c79c9
Content-Type: text/plain; charset=ISO-8859-1
Hi Daniel,
Both Gaussian and Gaussview will run on CentOS; I've got it working on an
Altix XE310 in my lab. A word of warning, though; if you get Gaussview, it
will only run on CentOS or Redhat. It doesn't run on Ubuntu, or any other
open-source Linux flavor (easily, at least).
Be well,
Jason
Jason S. D'Acchioli
Assistant Professor of Chemistry
University of Wisconsin-Stevens Point
On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|pace.edu <
owner-chemistry*o*ccl.net> wrote:
>
> Sent to CCL by: Daniel Strahs [dstrahs**pace.edu]
> Hello colleagues:
>
> Has any one had any experience installing Gaussian for Linux/Red Hat
> Enterprise on the Centos OS? The binary compatibility with RedHat
> interests us.
>
> Thanks for any responses!
>
> --
> Daniel B. Strahs
> Associate Professor
> Biology and Health Sciences Department
> Pace University, New York>
>
>
--00163630f5375a2c29049a4c79c9
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Hi Daniel,<br><br>Both Gaussian and Gaussview will run on CentOS; I've =
got it working on an Altix XE310 in my lab. A word of warning, though; if y=
ou get Gaussview, it will only run on CentOS or Redhat. It doesn't run =
on Ubuntu, or any other open-source Linux flavor (easily, at least). <br>
<br>Be well,<br><br>Jason<br><br>Jason S. D'Acchioli<br>Assistant Profe=
ssor of Chemistry <br>University of Wisconsin-Stevens Point<br><br><div cla=
ss=3D"gmail_quote">On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|=
<a href=3D"http://pace.edu">pace.edu</a> <span dir=3D"ltr"><<a href=3D"m=
ailto:owner-chemistry*o*ccl.net">owner-chemistry*o*ccl.net</a>></span> wrote=
:<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;"><br>
Sent to CCL by: Daniel Strahs [dstrahs**<a href=3D"http://pace.edu" target=
=3D"_blank">pace.edu</a>]<br>
Hello colleagues:<br>
<br>
Has any one had any experience installing Gaussian for Linux/Red Hat<br>
Enterprise on the Centos OS? The binary compatibility with RedHat<br>
interests us.<br>
<br>
Thanks for any responses!<br>
<br>
--<br>
Daniel B. Strahs<br>
Associate Professor<br>
Biology and Health Sciences Department<br>
Pace University, New York<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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<br>
<br>
</blockquote></div><br>
--00163630f5375a2c29049a4c79c9--
From owner-chemistry@ccl.net Thu Jan 20 17:58:01 2011
From: "richard apodaca rich_apodaca^yahoo.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: InChi converters
Message-Id: <-43713-110120140610-548-B9IqUzRrEs1IkdhyOR9K/A_._server.ccl.net>
X-Original-From: richard apodaca <rich_apodaca(0)yahoo.com>
Content-Transfer-Encoding: 8bit
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Date: Thu, 20 Jan 2011 11:05:52 -0800 (PST)
MIME-Version: 1.0
Sent to CCL by: richard apodaca [rich_apodaca:_:yahoo.com]
Hello Den,
Ninja is an open source toolkit for parsing InChIs:
http://depth-first.com/articles/2007/01/12/decoding-inchis-an-introduction-to-ninja/
It can be used as a command-line tool to report the structure of an InChI. Ninja can also be used as a library for writing InChI parsers.
Ninja was developed from scratch using the InChI technical documentation. As such, it's the only implementation of an InChI parser that I'm aware of that's fully independent of the IUPAC InChI code.
Best regards,
Rich
___________________________________
Richard L. Apodaca
http://depth-first.com Blog
http://metamolecular.com Company
--- On Thu, 1/20/11, Dennis Sprous dsprous=-=redpointbio.com <owner-chemistry|-|ccl.net> wrote:
> From: Dennis Sprous dsprous=-=redpointbio.com <owner-chemistry|-|ccl.net>
> Subject: CCL: InChi converters
> To: "Apodaca, Rich " <rich_apodaca|-|yahoo.com>
> Date: Thursday, January 20, 2011, 8:52 AM
>
> Sent to CCL by: "Dennis� Sprous"
> [dsprous()redpointbio.com]
>
> Dear All:
>
> I am interested in experiences with InChi to SDF or InChi
> to SMILES programs.� I am using OpenBabel 2.3.0 which
> is doing OK.� I am just wondering if there are other
> utilities out there.�
>
> -- Den
>
>
>
> -= This is automatically added to each message by the
> mailing script =-
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> please change
> the strange characters on the top line to the |-| sign. You
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> � � �> � � �> � � �>
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>
From owner-chemistry@ccl.net Thu Jan 20 18:33:01 2011
From: "Geoffrey Hutchison geoffh],[pitt.edu" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: complexes
Message-Id: <-43714-110120163509-26306-Su6PSnpgL+44fomx1Q5LfQ-,-server.ccl.net>
X-Original-From: Geoffrey Hutchison <geoffh^^pitt.edu>
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Date: Thu, 20 Jan 2011 16:34:53 -0500
MIME-version: 1.0 (Apple Message framework v1082)
Sent to CCL by: Geoffrey Hutchison [geoffh|,|pitt.edu]
> I discover that optimization with Avogadro gives varying coordinates and energies of the molecule with continuous click on the optimization option.
> How do I know when to stop optimizing? Because the coordinates I use in MOPAC calculations is the determinant of the accuracy of my results.
You are referring to the "auto-optimize" feature in Avogadro. This will continue to apply a particular force field method. In part, this provides interactive manipulation for a crude "dynamics" method (e.g., convert cyclohexane from chair to boat). It also allows you to modify the molecule while optimizing.
In general, if the energy appears stable, you are likely in a local minima and can submit to MOPAC or another program.
If you don't like the interactive optimization, Avogadro also offers a more traditional "Optimize Geometry" which will take a set number of steps (e.g., up to 500) and will stop early if the gradient or energy converges.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh..pitt.edu
web: http://hutchison.chem.pitt.edu/
From owner-chemistry@ccl.net Thu Jan 20 21:04:00 2011
From: "Jason Swails swails%qtp.ufl.edu" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian on Centos?
Message-Id: <-43715-110120180707-31052-9whWpCCMagMLNHD/2rmRyQ:-:server.ccl.net>
X-Original-From: Jason Swails <swails ~~ qtp.ufl.edu>
Content-Type: multipart/alternative; boundary=001517503b265e946c049a4f30c4
Date: Thu, 20 Jan 2011 18:06:51 -0500
MIME-Version: 1.0
Sent to CCL by: Jason Swails [swails!A!qtp.ufl.edu]
--001517503b265e946c049a4f30c4
Content-Type: text/plain; charset=ISO-8859-1
On Thu, Jan 20, 2011 at 2:52 PM, Jason D Acchioli jdacchio---gmail.com <
owner-chemistry]*[ccl.net> wrote:
> Hi Daniel,
>
> Both Gaussian and Gaussview will run on CentOS; I've got it working on an
> Altix XE310 in my lab. A word of warning, though; if you get Gaussview, it
> will only run on CentOS or Redhat. It doesn't run on Ubuntu, or any other
> open-source Linux flavor (easily, at least).
ooh! A challenge! Were it not for the hefty price tag I'd give it a go. An
ubuntu thread that may be helpful:
http://ubuntuforums.org/showthread.php?t=634578
In any case, Linux is Linux, so I can't imagine it's completely incompatible
with other flavors. It may be necessary to install additional packages with
the proper library versions.
As a side-note, SUSE 10 is listed as a supported platform if an additional
package is installed.
All the best,
Jason
>
> Be well,
>
> Jason
>
> Jason S. D'Acchioli
> Assistant Professor of Chemistry
> University of Wisconsin-Stevens Point
>
> On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|pace.edu <
> owner-chemistry],[ccl.net> wrote:
>
>>
>> Sent to CCL by: Daniel Strahs [dstrahs**pace.edu]
>> Hello colleagues:
>>
>> Has any one had any experience installing Gaussian for Linux/Red Hat
>> Enterprise on the Centos OS? The binary compatibility with RedHat
>> interests us.
>>
>> Thanks for any responses!
>>
>> --
>> Daniel B. Strahs
>> Associate Professor
>> Biology and Health Sciences Department
>> Pace University, New York>> E-mail to subscribers: CHEMISTRY],[ccl.net or use:>>
>> E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or use>>
>>
>>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
--001517503b265e946c049a4f30c4
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
<br><br><div class=3D"gmail_quote">On Thu, Jan 20, 2011 at 2:52 PM, Jason D=
Acchioli <a href=3D"http://jdacchio---gmail.com">jdacchio---gmail.com</a> =
<span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry]*[ccl.net">owner-chem=
istry]*[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;">Hi Daniel,<br><br>Both Gaussian and Gaussvi=
ew will run on CentOS; I've got it working on an Altix XE310 in my lab.=
A word of warning, though; if you get Gaussview, it will only run on CentO=
S or Redhat. It doesn't run on Ubuntu, or any other open-source Linux f=
lavor (easily, at least).</blockquote>
<div><br></div><div>ooh! A challenge! =A0Were it not for the hefty price ta=
g I'd give it a go. =A0An ubuntu thread that may be helpful: =A0<a href=
=3D"http://ubuntuforums.org/showthread.php?t=3D634578">http://ubuntuforums.=
org/showthread.php?t=3D634578</a></div>
<div><br></div><div>In any case, Linux is Linux, so I can't imagine it&=
#39;s completely incompatible with other flavors. =A0It may be necessary to=
install additional packages with the proper library versions.</div><div>
<br></div><div>As a side-note, SUSE 10 is listed as a supported platform if=
an additional package is installed.</div><div><br></div><div>All the best,=
<br>Jason</div><div><br></div><blockquote class=3D"gmail_quote" style=3D"ma=
rgin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>Be well,<br><br>Jason<br><br>Jason S. D'Acchioli<br>Assistant Profe=
ssor of Chemistry <br>University of Wisconsin-Stevens Point<br><br><div cla=
ss=3D"gmail_quote">On Wed, Jan 19, 2011 at 11:06 AM, Daniel Strahs dstrahs|=
<a href=3D"http://pace.edu" target=3D"_blank">pace.edu</a> <span dir=3D"ltr=
"><<a href=3D"mailto:owner-chemistry],[ccl.net" target=3D"_blank">owner-=
chemistry],[ccl.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left:1px solid rgb(204, 2=
04, 204);margin:0pt 0pt 0pt 0.8ex;padding-left:1ex"><br>
Sent to CCL by: Daniel Strahs [dstrahs**<a href=3D"http://pace.edu" target=
=3D"_blank">pace.edu</a>]<br>
Hello colleagues:<br>
<br>
Has any one had any experience installing Gaussian for Linux/Red Hat<br>
Enterprise on the Centos OS? The binary compatibility with RedHat<br>
interests us.<br>
<br>
Thanks for any responses!<br>
<br>
--<br>
Daniel B. Strahs<br>
Associate Professor<br>
Biology and Health Sciences Department<br>
Pace University, New York<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-
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<br>
</blockquote></div><br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jason M. Swails<br>Quan=
tum Theory Project,<br>University of Florida<br>Ph.D. Graduate Student<br>3=
52-392-4032<br>
--001517503b265e946c049a4f30c4--