From owner-chemistry@ccl.net Wed Nov 8 01:36:01 2006
From: "James Robinson James.Robinson[a]prosonix.co.uk" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: MD simulations using MMFF94x and MOE
Message-Id: <-32959-061107202621-123456-0dm2CA95KKNCZ9XrXWvlkA(a)server.ccl.net>
X-Original-From: "James Robinson" <James.Robinson::prosonix.co.uk>
Date: Wed, 8 Nov 2006 00:54:44 -0000
Sent to CCL by: "James Robinson" [James.Robinson[a]prosonix.co.uk]
Hi Sandeep,
There has been debate before about the implimentation of dynamics in
MOE. If memory serves Amber is often the preferred choice for MD of
polypeptides. However, the analysis tools in MOE are very useful. Allow
the calculation to run with some heating and try to use an end cooling
step. Make sure MOE writes structures to a moe.MDB file during the
simulation, it will get quite big, but MOE will handle it. That way you
can check dihedral angles, trans amide bonds, volume, and other
descriptors as you go. MOE may still lack some rigour in some
implimentations like dyanmics, but as tool that can serves as
qualitative/quantitative test for ideas in my opinion, it rocks!
James Robinson, Oxford, UK.
-----Original Message-----
From: Sandeep Kumar kumarsan(_)jhu.edu [mailto:owner-chemistry**ccl.net]
Sent: Tue 07/11/2006 18:55
To: James Robinson
Subject: CCL: MD simulations using MMFF94x and MOE
Sent to CCL by: "Sandeep Kumar" [kumarsan],[jhu.edu]
Dear Members:
I am trying to do MD calculations on a 28 residue peptide using MMFF94X
forcefield as implemented in MOE to assess its conformational
flexibility. I was wondering if somebody has experience of using MMFF94x
forcefield for peptide simulations and how does it compare with other
forcefields, say, AMBER or CHARMM? Another related question whether to
do implicit solvation or explicit solvation simulations? I mean which is
better and usually what should be the time scales for such simulations?
Any advices shall be greatly appreciated.
Yours sincerely,
Sandeep Kumar
-----------------------------------------------------------------------
Dr. Sandeep Kumar,
Associate Research Scientist,
Johns Hopkins University Department of Biology,
106 Mudd Hall, 3400 N. Charles Street,
Baltimore, MD 21218, USA.
Phone: 410-516-8433,
Email: kumarsan-.-jhu.edu.
URL: https://jshare.johnshopkins.edu/skumar23/public_html/
Previous URL: http://www.lecb.ncifcrf.gov/~kumarsan
From owner-chemistry@ccl.net Wed Nov 8 02:11:00 2006
From: "Gregory M Sandala sandala%%chem.usyd.edu.au" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL:G: SCRF errors with Gaussian
Message-Id: <-32960-061108005108-15246-g8UyD0ac1XNQvI+gsyRclg . server.ccl.net>
X-Original-From: "Gregory M Sandala" <sandala],[chem.usyd.edu.au>
Date: Wed, 8 Nov 2006 00:51:07 -0500
Sent to CCL by: "Gregory M Sandala" [sandala ~~ chem.usyd.edu.au]
Hello everyone. I'm trying to run some SCRF calculations with G03.D01 to generate charges for later
use in Amber. However, it appears as though generating the solute cavity is creating various
numerical instabilities. More specifically, I will get errors like:
Warning! T(1549,1799)=0.81795801D+02 is big!
T(1549,1549)=0.83983654D+02 T(1799,1799)=0.22200475D+02
Warning! T(****,****)=0.65648410D+38 is big!
T(****,****)=-.65648410D+38 T(****,****)=0.65648410D+38
Inv2 failed in DMIVCS.
Error termination via Lnk1e in /opt/g03d01/g03/l502.exe at Tue Oct 31 18:27:16 2006.
OR
------------------------------------------------------------------------------
Polarizable Continuum Model (PCM)
=================================
Model : PCM.
Atomic radii : UA0 (Simple United Atom Topological Model).
Polarization charges : Total charges.
Charge compensation : None.
Solution method : Matrix inversion.
Cavity : GePol (RMin=0.200 OFac=0.890).
Default sphere list used, NSphG= 92.
Tesserae with average area of 0.200 Ang**2.
Solvent : Diethylether, Eps = 4.335000
Eps(inf)= 0.000000
RSolv = 2.785000 Ang.
------------------------------------------------------------------------------
AdVTs1: ISph= 3199 is engulfed by JSph= 3202 but Ae( 3199) is not yet zero!
Error termination via Lnk1e in /opt/g03d01/g03/l301.exe at Mon Oct 30 18:07:11 2006.
The first error typically results when using radii=pauling and the second error occurs when using
the default radii (UA0). For the past week I've played with various parameters (PCM method, OFAC,
TSARE, etc.) but end up getting one of these errors. I'm becoming tired of 'playing' with these
numerous and varied parameters (it's all like black magic!) and am curious to know whether others
have come across such errors and, if so, how they managed to work around them. Thank you in
advance.
Best wishes,
Greg
--
Gregory M. Sandala
School of Chemistry
University of Sydney
Sydney NSW 2006
Australia
Ph: +61 2 9351 5361
sandala+*+chem.usyd.edu.au
From owner-chemistry@ccl.net Wed Nov 8 03:46:00 2006
From: "Igor Avilov avilovi###averell.umh.ac.be" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: Excited state electronic configurations
Message-Id: <-32961-061108034226-25144-9u4y63jukxpa1sb35jZX1g^-^server.ccl.net>
X-Original-From: "Igor Avilov" <avilovi * averell.umh.ac.be>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
charset="iso-8859-1"
Date: Wed, 8 Nov 2006 09:42:07 +0100
MIME-Version: 1.0
Sent to CCL by: "Igor Avilov" [avilovi]^[averell.umh.ac.be]
Dear Caroline,
If you are interested in population analysis in the excited states, you must use a two-step jobs like the one below:
%nproc=1
%mem=100MB
%Chk=HCl_cis
# CIS(Nstates=4)/STO-3G Test
Input created by Zoa v2.0 HCl_cis
0 1
Cl -0.000030 -0.645000 -0.000250
H 0.000030 0.645000 0.000250
--Link1--
%nproc=1
%mem=100MB
%Chk=HCl_cis
%NoSave
# CIS(Root=3,Read)/STO-3G Density=Current Pop=NPA Test
Input created by Zoa v2.0 HCl_cis
0 1
Cl -0.000030 -0.645000 -0.000250
H 0.000030 0.645000 0.000250
In this way you will get the populations for third excited state.
If you need populations for the first excited state, you can use a single-step job. Just include Density=Current keyword.
As far as I know it is not possible to get the density for time-dependent calculations (TD keyword).
I hope it help, although my answer may be incomplete.
Best wishes,
Igor Avilov.
-----Original Message-----
> From: owner-chemistry()ccl.net [mailto:owner-chemistry()ccl.net]
Sent: mardi 7 novembre 2006 18:15
To: Igor Avilov
Subject: CCL: Excited state electronic configurations
Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk]
Dear All,
I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated.
Thanks in advance,
Caroline Norris
cn29::sussex.ac.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
From owner-chemistry@ccl.net Wed Nov 8 04:49:01 2006
From: "Didier ROGNAN didier.rognan . pharma.u-strasbg.fr" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: atom renumbering
Message-Id: <-32962-061108044715-24071-rBPBFXdK2UEHKeWiLLcBpw+/-server.ccl.net>
X-Original-From: "Didier ROGNAN" <didier.rognan[*]pharma.u-strasbg.fr>
Date: Wed, 8 Nov 2006 04:47:14 -0500
Sent to CCL by: "Didier ROGNAN" [didier.rognan ~~ pharma.u-strasbg.fr]
Dear CCLers,
Has anyone a solution to automatically renumber atoms for a compound library sharing the same core structure such that all core atoms have a unique atom number ?
Many thanks for your anwser
Dr. Didier ROGNAN
Directeur de Recherche
CNRS UMR 7175-LC1
Institut Gilbert-Laustriat
74, route du Rhin, B.P.24
F-67401 Illkirch
direct line: +33 (0)3 90 24 42 35
secretary: +33(0)3 90 24 42 20
fax: +33 (0)3 90 24 43 10
email: didier.rognan]-[pharma.u-strasbg.fr
www:http://bioinfo-pharma.u-strasbg.fr
From owner-chemistry@ccl.net Wed Nov 8 07:21:00 2006
From: "Dr. Ponnadurai Ramasami ramchemi!A!intnet.mu" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: electron affinity
Message-Id: <-32963-061108062336-22918-Jk4LJqnQ/mUw6F1yBxONZw:server.ccl.net>
X-Original-From: "Dr. Ponnadurai Ramasami" <ramchemi{=}intnet.mu>
Content-Type: multipart/alternative;
boundary="----=_NextPart_000_0023_01C70348.29B78490"
Date: Wed, 8 Nov 2006 15:11:27 +0400
MIME-Version: 1.0
Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu]
This is a multi-part message in MIME format.
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Dear All
I am calculating the electron affinity of carbon monoxide using =
B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
I am getting a negative value of -100.2 kJ/mol.
The literature experimental value is 127.9 kJ/mol (I guess positive).
Is this correct?
Can electron affinity be negative?
I will appreciate in case someone can help.
Ramasami
=20
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<META http-equiv=3DContent-Type content=3D"text/html; =
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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear All</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I am calculating the electron affinity =
of carbon=20
monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20
negative).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I am getting a negative value of -100.2 =
kJ/mol.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>The literature experimental value is =
127.9 kJ/mol=20
(I guess positive).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Is this correct?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Can electron affinity be =
negative?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I will appreciate in case someone can=20
help.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Ramasami</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2> </DIV>
<DIV>
<TABLE style=3D"WIDTH: 240pt; BORDER-COLLAPSE: collapse" cellSpacing=3D0 =
cellPadding=3D0 width=3D320 border=3D0 x:str>
<COLGROUP>
<COL style=3D"WIDTH: 81pt; mso-width-source: userset; mso-width-alt: =
3949"=20
width=3D108>
<COL style=3D"WIDTH: 74pt; mso-width-source: userset; mso-width-alt: =
3620"=20
width=3D99>
<COL style=3D"WIDTH: 85pt; mso-width-source: userset; mso-width-alt: =
4132"=20
width=3D113>
<TBODY>
<TR style=3D"HEIGHT: 15.75pt" height=3D21>
<TD class=3Dxl24=20
style=3D"BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: =
#ece9d8; WIDTH: 240pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 15.75pt; =
BACKGROUND-COLOR: transparent"=20
width=3D320 colSpan=3D3 height=3D21><FONT color=3D#ff0000=20
size=3D2></FONT></TD></TR></TBODY></TABLE></DIV></FONT></BODY></HTML>
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From owner-chemistry@ccl.net Wed Nov 8 08:02:00 2006
From: "Soren Eustis soren__jhu.edu" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: electron affinity
Message-Id: <-32964-061108075735-26466-a4e1RSOr9LFRD2BhHkgQbg-#-server.ccl.net>
X-Original-From: "Soren Eustis" <soren|a|jhu.edu>
Content-Transfer-Encoding: 7bit
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charset="us-ascii"
Date: Wed, 8 Nov 2006 07:57:36 -0500
MIME-Version: 1.0
Sent to CCL by: "Soren Eustis" [soren/./jhu.edu]
Your method and basis set seem more than adequate. Electron affinity can
indeed be negative. However, in this case we know that is not true. I have
had much success calculating EA's using both DFT and MP2 - with a few
exceptions. A key thing to check is whether or not the multiplicity is
input correctly. For this case, I might see if MP2 or even HF describes
this system better. In fact, for this small of a molecule - one ought to be
able to run a CCSD(T) calculation in a fairly short time.
Regards,
Soren Eustis
-----Original Message-----
> From: owner-chemistry=ccl.net [mailto:owner-chemistry=ccl.net]
Sent: Wednesday, November 08, 2006 7:25 AM
To: Eustis, Soren
Subject: CCL: electron affinity
Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu]
This is a multi-part message in MIME format.
------=_NextPart_000_0023_01C70348.29B78490
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charset="Windows-1252"
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Dear All
I am calculating the electron affinity of carbon monoxide using =
B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
I am getting a negative value of -100.2 kJ/mol.
The literature experimental value is 127.9 kJ/mol (I guess positive).
Is this correct?
Can electron affinity be negative?
I will appreciate in case someone can help.
Ramasami
=20
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<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear All</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I am calculating the electron affinity =
of carbon=20
monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20
negative).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I am getting a negative value of -100.2 =
kJ/mol.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>The literature experimental value is =
127.9 kJ/mol=20
(I guess positive).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Is this correct?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Can electron affinity be =
negative?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I will appreciate in case someone can=20
help.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Ramasami</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2> </DIV>
<DIV>
<TABLE style=3D"WIDTH: 240pt; BORDER-COLLAPSE: collapse" cellSpacing=3D0 =
cellPadding=3D0 width=3D320 border=3D0 x:str>
<COLGROUP>
<COL style=3D"WIDTH: 81pt; mso-width-source: userset; mso-width-alt: =
3949"=20
width=3D108>
<COL style=3D"WIDTH: 74pt; mso-width-source: userset; mso-width-alt: =
3620"=20
width=3D99>
<COL style=3D"WIDTH: 85pt; mso-width-source: userset; mso-width-alt: =
4132"=20
width=3D113>
<TBODY>
<TR style=3D"HEIGHT: 15.75pt" height=3D21>
<TD class=3Dxl24=20
style=3D"BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: =
#ece9d8; WIDTH: 240pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 15.75pt; =
BACKGROUND-COLOR: transparent"=20
width=3D320 colSpan=3D3 height=3D21><FONT color=3D#ff0000=20
size=3D2></FONT></TD></TR></TBODY></TABLE></DIV></FONT></BODY></HTML>
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From owner-chemistry@ccl.net Wed Nov 8 08:36:00 2006
From: "Rafal A. Bachorz rafal.bachorz-*-chemie.uni-karlsruhe.de" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: electron affinity
Message-Id: <-32965-061108082518-14579-JtNA8j9XeB1A/V7pffb/hA:server.ccl.net>
X-Original-From: "Rafal A. Bachorz" <rafal.bachorz**chemie.uni-karlsruhe.de>
Content-Transfer-Encoding: 7bit
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Date: Wed, 08 Nov 2006 14:26:26 +0100
MIME-Version: 1.0
Sent to CCL by: "Rafal A. Bachorz" [rafal.bachorz*_*chemie.uni-karlsruhe.de]
Dear Dr. Ponnadurai Ramasami,
> I am calculating the electron affinity of carbon monoxide using =
> B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
Do you use the same geometry for the neutral and anion? Normally there
is some geometry relaxation upon electron attachment. When you use
optimal geometries of neutral and anion, then you can calculate
adiabatic electron affinity (AEA), which is defined
AEA = E(N .. N) - E(A .. A),
where the E(N .. N) and E(A .. A) are energies of the neutral and anion
calculated at their optimal geometries corrected with the zero point
vibration energies (ZPVE). It is important to take into account usually
non-zero (and sometimes significant) contributions from ZPVE.
> I am getting a negative value of -100.2 kJ/mol.
> The literature experimental value is 127.9 kJ/mol (I guess positive).
That is probably AEA, but I am not 100% sure.
> Is this correct?
I do not know, check the geometries.
> Can electron affinity be negative?
If the adiabatic electron affinity is negative, then it means that the
E(A .. A) is higher than E(N .. N). That is of course possible.
Best regards,
Rafal Bachorz
--
www.bachorz.eu
From owner-chemistry@ccl.net Wed Nov 8 09:11:00 2006
From: "Dr. Ponnadurai Ramasami ramchemi,+,intnet.mu" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: anharmonic constant
Message-Id: <-32966-061108064117-2863-LZX5rjU6WeuiJitTQimYNQ%%server.ccl.net>
X-Original-From: "Dr. Ponnadurai Ramasami" <ramchemi|a|intnet.mu>
Content-Type: multipart/alternative;
boundary="----=_NextPart_000_000D_01C7034A.BC8403A0"
Date: Wed, 8 Nov 2006 15:29:52 +0400
MIME-Version: 1.0
Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi#intnet.mu]
This is a multi-part message in MIME format.
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Dear All
I did a frequency calculation for carbon monoxide.
#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3DVibRot maxdisk=3D2gb
or
#P b3lyp/6-311++G(2df,2pd) opt=3Dtight freq=3Danharm maxdisk=3D2gb
However for this diatomic molecule, the anharmonic constant does not =
appear in the output, although it appears for a triatomic molecule.
Can anyone help?
Thanks
Ramasami
=20
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
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<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear All</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I did a frequency calculation for =
carbon=20
monoxide.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>#P b3lyp/6-311++G(2df,2pd) opt=3Dtight =
freq=3DVibRot=20
maxdisk=3D2gb</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>or</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>#P b3lyp/6-311++G(2df,2pd) opt=3Dtight =
freq=3Danharm=20
maxdisk=3D2gb</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>However for this diatomic molecule, the =
anharmonic=20
constant does not appear in the output, although it appears for a =
triatomic=20
molecule.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Can anyone help?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thanks</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Ramasami</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2> </DIV>
<DIV>
<TABLE style=3D"WIDTH: 240pt; BORDER-COLLAPSE: collapse" cellSpacing=3D0 =
cellPadding=3D0 width=3D320 border=3D0 x:str>
<COLGROUP>
<COL style=3D"WIDTH: 81pt; mso-width-source: userset; mso-width-alt: =
3949"=20
width=3D108>
<COL style=3D"WIDTH: 74pt; mso-width-source: userset; mso-width-alt: =
3620"=20
width=3D99>
<COL style=3D"WIDTH: 85pt; mso-width-source: userset; mso-width-alt: =
4132"=20
width=3D113>
<TBODY>
<TR style=3D"HEIGHT: 15.75pt" height=3D21>
<TD class=3Dxl24=20
style=3D"BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: =
#ece9d8; WIDTH: 240pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 15.75pt; =
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From owner-chemistry@ccl.net Wed Nov 8 09:47:00 2006
From: "Szabolcs Csepregi scsepregi~~chemaxon.com" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: atom renumbering
Message-Id: <-32967-061108091032-4606-5XbS3XDiYTqxKukhpZvAbw]-[server.ccl.net>
X-Original-From: Szabolcs Csepregi <scsepregi||chemaxon.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Wed, 08 Nov 2006 15:10:26 +0100
MIME-Version: 1.0
Sent to CCL by: Szabolcs Csepregi [scsepregi###chemaxon.com]
Dear Didier,
It is relatively easy to write a program for this with the use of JChem API.
See example code at the end of this discussion on our forum:
(atomrearranger.java)
http://www.chemaxon.com/forum/ftopic519.html
And you can create the atom ordering using substructure search:
http://www.chemaxon.com/jchem/doc/guide/search/index.html#searchmem
Best regards,
Szabolcs
Szabolcs Csepregi, PhD
Director of Search Technologies, ChemAxon Ltd.
http://www.chemaxon.com
Skype: szabolcs.csepregi
Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659
Didier ROGNAN didier.rognan . pharma.u-strasbg.fr wrote:
> Sent to CCL by: "Didier ROGNAN" [didier.rognan ~~ pharma.u-strasbg.fr]
> Dear CCLers,
>
>
> Has anyone a solution to automatically renumber atoms for a compound library sharing the same core structure such that all core atoms have a unique atom number ?
>
>
> Many thanks for your anwser
>
> Dr. Didier ROGNAN
> Directeur de Recherche
> CNRS UMR 7175-LC1
> Institut Gilbert-Laustriat
> 74, route du Rhin, B.P.24
> F-67401 Illkirch
>
> direct line: +33 (0)3 90 24 42 35
> secretary: +33(0)3 90 24 42 20
> fax: +33 (0)3 90 24 43 10
> email: didier.rognan() pharma.u-strasbg.fr
> www:http://bioinfo-pharma.u-strasbg.fr>
>
>
>
>
From owner-chemistry@ccl.net Wed Nov 8 10:34:00 2006
From: "Mikael Johansson mikael.johansson+/-helsinki.fi" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: electron affinity
Message-Id: <-32968-061108102935-20408-xYRX9frJVm2UE4C0As6OmQ|,|server.ccl.net>
X-Original-From: Mikael Johansson <mikael.johansson[-]helsinki.fi>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Wed, 8 Nov 2006 17:29:28 +0200 (EET)
MIME-Version: 1.0
Sent to CCL by: Mikael Johansson [mikael.johansson]_[helsinki.fi]
Hello Ramasami and All!
On Wed, 8 Nov 2006, Dr. Ponnadurai Ramasami ramchemi!A!intnet.mu wrote:
> I am calculating the electron affinity of carbon monoxide using =
> B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
> I am getting a negative value of -100.2 kJ/mol.
> The literature experimental value is 127.9 kJ/mol (I guess positive).
>
> Is this correct?
> Can electron affinity be negative?
The sign should at least be correct; the CO anion is not stable. The
following paper might be of interest:
A. Dreuw, L. S. Cederbaum, "Long-lived high-spin states of small anions:
6PI state of CO-", Phys. Rev. A 59 (1999) 2702-2706.
Have a nice day,
Mikael J.
http://www.iki.fi/~mpjohans/
From owner-chemistry@ccl.net Wed Nov 8 11:09:00 2006
From: "Tanja van Mourik tanja.vanmourik:st-andrews.ac.uk" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: electron affinity
Message-Id: <-32969-061108104819-2819-K6tbzA+jmQQZK8dJikFcNg^-^server.ccl.net>
X-Original-From: Tanja van Mourik <tanja.vanmourik-$-st-andrews.ac.uk>
Content-Transfer-Encoding: 8bit
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Date: Wed, 8 Nov 2006 15:47:15 +0000
MIME-Version: 1.0
Sent to CCL by: Tanja van Mourik [tanja.vanmourik*|*st-andrews.ac.uk]
Hi Ramasami,
You may be interested in the following book chapter:
"Calculation of Electron Affinities. A Roadmap"
T.H. Dunning, K.A. Peterson and T. van Mourik
in The Dissociative Recombination of Molecules with Electrons, Ed. S. L.
Guberman, (Kluwer Academic/Plenum Publishers, New York, 2002).
Here we compared the accuracy of different methods (CISD, MPn, coupled cluster
methods) and basis sets for the electron affinities of CN and O2. The electron
affinities converge slowly with basis set, so large basis sets (with diffuse
functions) are important. CCSD(T) gives electron affinities that are (almost)
within chemical accuracy. Although DFT methods were not included in this
investigation, based on the inconsistent results obtained with CCSD and MP2
(MP2 underestimates in one case and overestimates in the other), I would not
expect B3LYP to give consistently reliable results for electron affinities. As
also recommended by Soren, for a system of this size it would be best to use
CCSD(T), or CCSDT if feasible, in combination with a basis set like
aug-cc-pVQZ/5Z.
Hope this helps,
Tanja
--
=================================================================
Tanja van Mourik
Royal Society University Research Fellow
School of Chemistry, University of St. Andrews
North Haugh, St. Andrews
Fife KY16 9ST, Scotland (UK)
email: tanja.vanmourik:+:st-andrews.ac.uk
web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm
=================================================================
> Sent to CCL by: "Soren Eustis" [soren/./jhu.edu]
> Your method and basis set seem more than adequate. Electron affinity can
> indeed be negative. However, in this case we know that is not true. I have
> had much success calculating EA's using both DFT and MP2 - with a few
> exceptions. A key thing to check is whether or not the multiplicity is
> input correctly. For this case, I might see if MP2 or even HF describes
> this system better. In fact, for this small of a molecule - one ought to be
> able to run a CCSD(T) calculation in a fairly short time.
>
> Regards,
>
> Soren Eustis
>
>
> -----Original Message-----
> > From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net]
> Sent: Wednesday, November 08, 2006 7:25 AM
> To: Eustis, Soren
> Subject: CCL: electron affinity
>
> Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu]
> This is a multi-part message in MIME format.
>
> ------=_NextPart_000_0023_01C70348.29B78490
> Content-Type: text/plain;
> charset="Windows-1252"
> Content-Transfer-Encoding: quoted-printable
>
> Dear All
>
> I am calculating the electron affinity of carbon monoxide using =
> B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
> I am getting a negative value of -100.2 kJ/mol.
> The literature experimental value is 127.9 kJ/mol (I guess positive).
>
> Is this correct?
> Can electron affinity be negative?
>
> I will appreciate in case someone can help.
>
> Ramasami
>
>
>
>
> =20
>
>
> ------=_NextPart_000_0023_01C70348.29B78490
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> charset="Windows-1252"
> Content-Transfer-Encoding: quoted-printable
>
> <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
> <HTML><HEAD>
> <META http-equiv=3DContent-Type content=3D"text/html; =
> charset=3Dwindows-1252">
> <META content=3D"MSHTML 6.00.2600.0" name=3DGENERATOR>
> <STYLE></STYLE>
> </HEAD>
> <BODY bgColor=3D#ffffff>
> <DIV><FONT face=3DArial size=3D2>Dear All</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>I am calculating the electron affinity =
> of carbon=20
> monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20
> negative).</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2>I am getting a negative value of -100.2 =
>
> kJ/mol.</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2>The literature experimental value is =
> 127.9 kJ/mol=20
> (I guess positive).</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>Is this correct?</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2>Can electron affinity be =
> negative?</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>I will appreciate in case someone can=20
> help.</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>Ramasami</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2> </DIV>
> <DIV>
> <TABLE style=3D"WIDTH: 240pt; BORDER-COLLAPSE: collapse" cellSpacing=3D0 =
>
> cellPadding=3D0 width=3D320 border=3D0 x:str>
> <COLGROUP>
> <COL style=3D"WIDTH: 81pt; mso-width-source: userset; mso-width-alt: =
> 3949"=20
> width=3D108>
> <COL style=3D"WIDTH: 74pt; mso-width-source: userset; mso-width-alt: =
> 3620"=20
> width=3D99>
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> 4132"=20
> width=3D113>
> <TBODY>
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> <TD class=3Dxl24=20
> style=3D"BORDER-RIGHT: #ece9d8; BORDER-TOP: #ece9d8; BORDER-LEFT: =
> #ece9d8; WIDTH: 240pt; BORDER-BOTTOM: #ece9d8; HEIGHT: 15.75pt; =
> BACKGROUND-COLOR: transparent"=20
> width=3D320 colSpan=3D3 height=3D21><FONT color=3D#ff0000=20
> size=3D2></FONT></TD></TR></TBODY></TABLE></DIV></FONT></BODY></HTML>
>
>
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>
>
>
>
--
=================================================================
Tanja van Mourik
Royal Society University Research Fellow
School of Chemistry, University of St. Andrews
North Haugh, St. Andrews
Fife KY16 9ST, Scotland (UK)
email: tanja.vanmourik:+:st-andrews.ac.uk
web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm
=================================================================
------------------------------------------------------------------
University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
From owner-chemistry@ccl.net Wed Nov 8 11:44:01 2006
From: "Frank Jensen frj!^!ifk.sdu.dk" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: SV: electron affinity
Message-Id: <-32970-061108084817-30981-7pM2iJwIQ8u5BqyAUo/oFw.@.server.ccl.net>
X-Original-From: "Frank Jensen" <frj##ifk.sdu.dk>
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charset="us-ascii"
Date: Wed, 8 Nov 2006 14:46:59 +0100
MIME-Version: 1.0
Sent to CCL by: "Frank Jensen" [frj+/-ifk.sdu.dk]
Beware that the EA calculated by DFT in most cases is _not_ a
well-defined quantity. For most systems the extra electron in anions is
not bound, _if_ a sufficiently flexible basis set is used. For
(augmented) DZ and TZ type basis sets, this shows up as positive HOMO
energies. If the HOMO is positive, the electron is not bound, and if you
add enough diffuse basis functions, the extra electron detaches from the
molecule. In other words, you can get essentially any result you want by
choosing the basis set.
There are a few exceptions, like CN- and perhaps also F-, where the EA
is sufficiently large that the extra electron is bound, but CO-
certainly does not belong to this class.
With this being said, there is a large body of computational evidence
showing that methods like B3LYP with a DZ or TZ type basis set augmented
with diffuse functions (like aug-cc-pVDZ or 6-311+G**) does a fairly
good job at reproducing the experimental EA results. The reason is that
the limited basis set constrains the extra electron to be in roughly the
right physical space, and the functional does a reasonable job at
estimating the energy of this confined electron density. This gives you
a reasonable estimate for the right physical reasons, but not for the
right theoretical reasons.
Check your HOMO energy for the anion. If it is positive, you are relying
on 'good' results due to error cancellations and a lucky choice of
functional and basis set, and sometimes your luck runs out.....
Frank
-----Oprindelig meddelelse-----
Fra: owner-chemistry(a)ccl.net [mailto:owner-chemistry(a)ccl.net]
Sendt: Wednesday, November 08, 2006 2:11 PM
Emne: CCL: electron affinity
Sent to CCL by: "Soren Eustis" [soren/./jhu.edu]
Your method and basis set seem more than adequate. Electron affinity
can
indeed be negative. However, in this case we know that is not true. I
have
had much success calculating EA's using both DFT and MP2 - with a few
exceptions. A key thing to check is whether or not the multiplicity is
input correctly. For this case, I might see if MP2 or even HF describes
this system better. In fact, for this small of a molecule - one ought
to be
able to run a CCSD(T) calculation in a fairly short time.
Regards,
Soren Eustis
-----Original Message-----
> From: owner-chemistry:_:ccl.net [mailto:owner-chemistry:_:ccl.net]
Sent: Wednesday, November 08, 2006 7:25 AM
To: Eustis, Soren
Subject: CCL: electron affinity
Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu]
This is a multi-part message in MIME format.
------=_NextPart_000_0023_01C70348.29B78490
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charset="Windows-1252"
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Dear All
I am calculating the electron affinity of carbon monoxide using =
B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
I am getting a negative value of -100.2 kJ/mol.
The literature experimental value is 127.9 kJ/mol (I guess positive).
Is this correct?
Can electron affinity be negative?
I will appreciate in case someone can help.
Ramasami
=20
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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear All</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I am calculating the electron affinity
=
of carbon=20
monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO,=20
negative).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I am getting a negative value of -100.2
=
kJ/mol.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>The literature experimental value is =
127.9 kJ/mol=20
(I guess positive).</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Is this correct?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Can electron affinity be =
negative?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I will appreciate in case someone
can=20
help.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Ramasami</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2> </DIV>
<DIV>
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cellPadding=3D0 width=3D320 border=3D0 x:str>
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ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://w
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From owner-chemistry@ccl.net Wed Nov 8 12:19:00 2006
From: "Emi Psachoulia efthymia.psachoulia^-^merton.ox.ac.uk" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian calculation
Message-Id: <-32971-061108085626-31805-FCAKmUIC8TfIw9ZVsjma7g _ server.ccl.net>
X-Original-From: "Emi Psachoulia" <efthymia.psachoulia%%merton.ox.ac.uk>
Date: Wed, 8 Nov 2006 08:56:26 -0500
Sent to CCL by: "Emi Psachoulia" [efthymia.psachoulia!A!merton.ox.ac.uk]
Hi,
I tried to use Gaussian03 to do geometrical optimization of a phosphate anion and then to calculate its charges.
I used for the geometry calculation HF/6-31G(d) Opt NoSymm and HF/6-31G(d,p) Opt NoSymm and then for the charge HF/6-31G* pop=mk iop(6/33=2) and HF/6-31G** pop=mk iop(6/33=2) respectively.
I had an output for the geometry calculations, but not for the charges.
I would like to ask you what the multiplicity is for system given that electrons delocalised.
Also, what basis set shall I use?
Thank you,
Emi Psachoulia
efthymia.psachoulia/a\merton.ox.ac.uk
From owner-chemistry@ccl.net Wed Nov 8 12:54:00 2006
From: "polosan silviu spol68__yahoo.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: Excited state electronic configurations
Message-Id: <-32972-061107202621-23108-8Ox79JUWeX2Ohf0eAAAh/Q .. server.ccl.net>
X-Original-From: polosan silviu <spol68^-^yahoo.com>
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Date: Tue, 7 Nov 2006 17:26:14 -0800 (PST)
MIME-Version: 1.0
Sent to CCL by: polosan silviu [spol68]=[yahoo.com]
--0-1378242960-1162949174=:88350
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What kind of command line you used? I mean method and basic set?
Silviu
"Caroline Norris cn29---sussex.ac.uk" <owner-chemistry_._ccl.net> wrote:
Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk]
Dear All,
I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated.
Thanks in advance,
Caroline Norris
cn29::sussex.ac.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtDr. Silviu POLOSAN
Faculty of Engineering, Kyoto Sangyo University, Kyoto 603-8555, Japan
e-mails: polosan_._cc.kyoto-su.ac.jp;
silv_._infim.ro
---------------------------------
Sponsored Link
Mortgage rates near historic lows: $150,000 loan as low as $579/mo. Intro-*Terms
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<div>What kind of command line you used? I mean method and basic set?</div> <div> </div> <div>Silviu<BR><BR><B><I>"Caroline Norris cn29---sussex.ac.uk" <owner-chemistry_._ccl.net></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Sent to CCL by: "Caroline Norris" [cn29::sussex.ac.uk]<BR>Dear All,<BR>I am in the process of calculating the potential energy curves of the lowest lying excited state of neutral vanadium oxide, and I was wondering if there's any way to determine the electronic configuration of the excited states. I've been using the pop=npa keyword, but this only details the ground state of the complex. Any help would be greatly appreciated.<BR>Thanks in advance,<BR>Caroline Norris<BR>cn29::sussex.ac.uk<BR><BR><BR><BR<BR<BR<BR<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/chemistry/sub_unsub.shtml<BR><BR<BR><BR<BR<BR><BR<BR><BR<BR>http://www.ccl.net/spammers.txt<BR><BR<BR><BR<BR><BR><BR><BR></BLOCKQUOTE><BR><BR><BR>Dr. Silviu POLOSAN<br>Faculty of
Engineering, Kyoto Sangyo University, Kyoto 603-8555, Japan<br>e-mails: polosan_._cc.kyoto-su.ac.jp;<br> silv_._infim.ro<p> 
<hr size=1>Sponsored Link<br><a href="https://www2.nextag.com/goto.jsp?product=100000035&url=/st.jsp&tm=y&search=b_historiclows170k&s=3968&p=5035&disc=y&vers=687"><br>Mortgage rates near historic lows: $150,000 loan as low as $579/mo. Intro-*Terms</a>
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From owner-chemistry@ccl.net Wed Nov 8 13:29:00 2006
From: "Gregory Sandala sandala._._.rsc.anu.edu.au" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: electron affinity
Message-Id: <-32973-061108083013-15796-PJ38Tf6+K1/W+rc2nK698w_._server.ccl.net>
X-Original-From: Gregory Sandala <sandala,,rsc.anu.edu.au>
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Sent to CCL by: Gregory Sandala [sandala..rsc.anu.edu.au]
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You will find this resource helpful:
http://webbook.nist.gov/chemistry/ion/#EA
Best wishes,
Greg
On 08/11/2006, at 1:21 PM, Dr. Ponnadurai Ramasami ramchemi!A!
intnet.mu wrote:
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> Dear All
>
> I am calculating the electron affinity of carbon monoxide using =
> B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
> I am getting a negative value of -100.2 kJ/mol.
> The literature experimental value is 127.9 kJ/mol (I guess positive).
>
> Is this correct?
> Can electron affinity be negative?
>
> I will appreciate in case someone can help.
>
> Ramasami
>
>
>
>
> =20
>
>
> ------=_NextPart_000_0023_01C70348.29B78490
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> charset="Windows-1252"
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> charset=3Dwindows-1252">
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> <STYLE></STYLE>
> </HEAD>
> <BODY bgColor=3D#ffffff>
> <DIV><FONT face=3DArial size=3D2>Dear All</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>I am calculating the electron
> affinity =
> of carbon=20
> monoxide using B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E
> (CO,=20
> negative).</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2>I am getting a negative value of
> -100.2 =
>
> kJ/mol.</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2>The literature experimental value
> is =
> 127.9 kJ/mol=20
> (I guess positive).</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>Is this correct?</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2>Can electron affinity be =
> negative?</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>I will appreciate in case someone
> can=20
> help.</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2>Ramasami</FONT></DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
> <DIV><FONT face=3DArial size=3D2></FONT> </DIV>
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> 3949"=20
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> 3620"=20
> width=3D99>
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---
Gregory M. Sandala
School of Chemistry
University of Sydney
Sydney NSW 2006
Australia
Ph: +61 2 9351 5361
sandala!A!chem.usyd.edu.au
--Apple-Mail-2--430443
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<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; ">You will find this resource =
helpful:<DIV><BR class=3D"khtml-block-placeholder"></DIV><DIV><A =
href=3D"http://webbook.nist.gov/chemistry/ion/#EA">http://webbook.nist.gov=
/chemistry/ion/#EA</A></DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Best =
wishes,</DIV><DIV>Greg</DIV><DIV><BR><DIV><DIV>On 08/11/2006, at 1:21 =
PM, Dr. Ponnadurai Ramasami ramchemi!A!intnet.mu wrote:</DIV><BR =
class=3D"Apple-interchange-newline"><BLOCKQUOTE type=3D"cite"><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Sent to CCL by: "Dr. Ponnadurai Ramasami" =
[ramchemi-#-intnet.mu]</DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; ">This is a multi-part =
message in MIME format.</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; =
">------=3D_NextPart_000_0023_01C70348.29B78490</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Content-Type: text/plain;</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><SPAN class=3D"Apple-tab-span" =
style=3D"white-space:pre"> </SPAN>charset=3D"Windows-1252"</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Content-Transfer-Encoding: =
quoted-printable</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Dear All</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">I am calculating the electron =
affinity of carbon monoxide using =3D</DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, =
negative).</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">I am getting a negative value of =
-100.2 kJ/mol.</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">The literature experimental =
value is 127.9 kJ/mol (I guess positive).</DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Is this =
correct?</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">Can electron affinity be =
negative?</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">I will appreciate in case someone can =
help.</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Ramasami</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN =
class=3D"Apple-converted-space">=A0 =A0 </SPAN>=3D20</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">------=3D_NextPart_000_0023_01C70348.29B78490</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">Content-Type: text/html;</DIV><DIV =
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quoted-printable</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 =
Transitional//EN"></DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; =
"><HTML><HEAD></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><META =
http-equiv=3D3DContent-Type content=3D3D"text/html; =3D</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">charset=3D3Dwindows-1252"></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><META content=3D3D"MSHTML 6.00.2600.0" =
name=3D3DGENERATOR></DIV><DIV style=3D"margin-top: 0px; margin-right: =
0px; margin-bottom: 0px; margin-left: 0px; =
"><STYLE></STYLE></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"></HEAD></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><BODY =
bgColor=3D3D#ffffff></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial size=3D3D2>Dear =
All</FONT></DIV></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial =
size=3D3D2></FONT>&nbsp;</DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial size=3D3D2>I =
am calculating the electron affinity =3D</DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">of =
carbon=3D20</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">monoxide using B3LYP/aug-cc-pVTZ =
by evaluating E(CO, neutral) - E(CO,=3D20</DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">negative).</FONT></DIV></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial size=3D3D2>I am getting a =
negative value of -100.2 =3D</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =
14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; =
">kJ/mol.</FONT></DIV></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial size=3D3D2>The literature =
experimental value is =3D</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">127.9 =
kJ/mol=3D20</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">(I guess =
positive).</FONT></DIV></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial =
size=3D3D2></FONT>&nbsp;</DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial size=3D3D2>Is =
this correct?</FONT></DIV></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial size=3D3D2>Can electron affinity =
be =3D</DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; =
">negative?</FONT></DIV></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial =
size=3D3D2></FONT>&nbsp;</DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial size=3D3D2>I =
will appreciate in case someone can=3D20</DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">help.</FONT></DIV></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV><FONT face=3D3DArial =
size=3D3D2></FONT>&nbsp;</DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial =
size=3D3D2>Ramasami</FONT></DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial =
size=3D3D2></FONT>&nbsp;</DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial =
size=3D3D2></FONT>&nbsp;</DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial =
size=3D3D2></FONT>&nbsp;</DIV></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; "><DIV><FONT face=3D3DArial =
size=3D3D2>&nbsp;</DIV></DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
"><DIV></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; "><TABLE style=3D3D"WIDTH: =
240pt; BORDER-COLLAPSE: collapse" cellSpacing=3D3D0 =3D</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style=3D"margin-top: =
0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =
">cellPadding=3D3D0 width=3D3D320 border=3D3D0 x:str></DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
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margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN =
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81pt; mso-width-source: userset; mso-width-alt: =3D</DIV><DIV =
style=3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =
margin-left: 0px; ">3949"=3D20</DIV><DIV style=3D"margin-top: 0px; =
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN =
class=3D"Apple-converted-space">=A0 </SPAN>width=3D3D108></DIV><DIV =
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0px; margin-bottom: 0px; margin-left: 0px; ">3620"=3D20</DIV><DIV =
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85pt; mso-width-source: userset; mso-width-alt: =3D</DIV><DIV =
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14px; "><BR></DIV><DIV style=3D"margin-top: 0px; margin-right: 0px; =
margin-bottom: 0px; margin-left: 0px; ">-=3D This is automatically added =
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From owner-chemistry@ccl.net Wed Nov 8 14:03:00 2006
From: "Karl Irikura karl.irikura- -nist.gov" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL:G: electron affinity
Message-Id: <-32974-061108102338-19952-ad+1GNE3jQhWx4rW1xOZcQ_-_server.ccl.net>
X-Original-From: Karl Irikura <karl.irikura]-[nist.gov>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Date: Wed, 08 Nov 2006 08:54:05 -0500
Mime-Version: 1.0
Sent to CCL by: Karl Irikura [karl.irikura-x-nist.gov]
Hi. In the chemistry WebBook (http://webbook.nist.gov/chemistry/)
the EA is listed as 1.3261 eV (or 127.95 kJ/mol) but there is an
annotation by John Bartmess (Univ. Tennessee) that G3(MP2)
calculations predict the anion to be unbound by > 1.5 eV (> 140
kJ/mol). Your calculation also predicts the anion to be
unbound. There is a paper by EPF Lee et al. [CPL 336(5-6) 479
(2001)] concluding that the anion is unstable. So your result
appears qualitatively correct. The actual value you get will depend
strongly upon the basis set. Try it! Add (in Gaussian, keyword is
"extrabasis") a diffuse s-function with exponent of 0.0001 to the
basis set on one of the atoms. The calculated EA should get close to
zero; the diffuse function mimics a continuum function, allowing the
added electron to avoid the molecule.
Electron affinity, as a thermodynamic quantity, must be non-negative
(unless, arguably, a metastable anion is long-lived; see Lee's paper,
or papers by L-S Wang about multiply charged anions). But sometimes
resonances in electron scattering are loosely described as states of
negative electron affinity.
Regards,
Karl
At 07:39 AM 11/8/2006, you wrote:
>Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi-#-intnet.mu]
>This is a multi-part message in MIME format.
>
>------=_NextPart_000_0023_01C70348.29B78490
>Content-Type: text/plain;
> charset="Windows-1252"
>Content-Transfer-Encoding: quoted-printable
>
>Dear All
>
>I am calculating the electron affinity of carbon monoxide using =
>B3LYP/aug-cc-pVTZ by evaluating E(CO, neutral) - E(CO, negative).
>I am getting a negative value of -100.2 kJ/mol.
>The literature experimental value is 127.9 kJ/mol (I guess positive).
>
>Is this correct?
>Can electron affinity be negative?
>
>I will appreciate in case someone can help.
>
>Ramasami
>
>
>-----=_NextPart_000_0023_01C70348.29B78490------------------------------------------------
Dr. Karl K. Irikura
National Institute of Standards and Technology
100 Bureau Drive, Stop 8380
Gaithersburg, MD 20899-8380
voice: 301-975-2510 fax: 301-869-4020
e-mail: karl.irikura#%#nist.gov
http://www.nist.gov/compchem/
----------------------------------------------
From owner-chemistry@ccl.net Wed Nov 8 14:39:00 2006
From: "Hugo O Villar hugo:+:altoris.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: SARvision- New Release
Message-Id: <-32975-061108115940-8976-XZRDMublr/wV0SdRz5ONvw^_^server.ccl.net>
X-Original-From: "Hugo O Villar" <hugo-x-altoris.com>
Date: Wed, 8 Nov 2006 11:59:39 -0500
Sent to CCL by: "Hugo O Villar" [hugo*_*altoris.com]
CCLers,
In the past some people from this list have expressed an interest in SARvision, our chemoinformatics software. Some of you are already users. We have just had a new release, version 2.4. If you are interested, you can get a demo of the product by visiting our website www.chemapps.com and clicking on the Products tab. There is an active link to download the demo. The demo is fully functional for 2 weeks. There you can also find a link that outlines what is new in this version.
SARvision is a desktop software application that identifies chemical motifs present in chemical datasets and organizes available biological and biochemical data, such as those that may result from high throughput screening, according to the scaffolds it identifies. The program facilitates R-table generation and facilitates data reporting as well. The user can quickly navigate chemical information and create tables with the data available that can be exported into applications such as Microsoft Word and Excel. Among the new features, we have comparison of the scaffold content of different libraries, added graphical capabilities to plot properties by scaffolds
A Linux version (without GUI)for scaffold identification is also available if you let meknow you are interested. SARvision is used by chemoinformaticians, medicinal chemists, high throughput screeners and even patent agents.
Thanks!
Hugo
===========================
Hugo O. Villar, Ph.D.
Chemapps, An Altoris Project.
11575 Sorrento Valley Road 214
San Diego, CA 92121
858.259.8161 Phone
858.259.8162 Fax
www.altoris.com
www.chemapps.com