From owner-chemistry@ccl.net Wed Aug 9 04:21:00 2006
From: "Jens Spanget-Larsen spanget[#]ruc.dk" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL:G: MP2 HOMO-LUMO gap with G03
Message-Id: <-32360-060809042014-28654-VuoLzDvpiTG3C5WXY7inMQ[A]server.ccl.net>
X-Original-From: Jens Spanget-Larsen <spanget###ruc.dk>
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Date: Wed, 09 Aug 2006 10:20:01 +0200
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Sent to CCL by: Jens Spanget-Larsen [spanget:-:ruc.dk]
Dear Herbert,
the MP2 procedure uses the orbitals produced by a HF calculation so the
HOMO-LUMO gap should be excactly the same (provided the same basis set
is used). The orbitals of a DFT calculation are the so-called Kohn-Sham
orbitals, and they are conceptually different from HF orbitals. - Yes, a
better way to predict electronic excitation energies would be to use CIS
or TD-DFT. In particular, TD-DFT frequently works beautifully. See
f.inst. J. Fabian et al., J. Mol. Struct. (Theochem) 594, 41-53 (2002).
Jens >--<
------------------------------------------------------
JENS SPANGET-LARSEN Office: +45 4674 2710
Department of Chemistry Fax: +45 4674 3011
Roskilde University (RUC) Mobile: +45 2320 6246
P.O.Box 260 E-Mail: spanget%ruc.dk
DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget
------------------------------------------------------
Herbert Fruchtl herbert.fruchtl*_*st-andrews.ac.uk wrote:
> Sent to CCL by: "Herbert Fruchtl" [herbert.fruchtl!^!st-andrews.ac.uk]
> Something I should probably know, but...
>
> I am calculating the HOMO-LUMO gap of small organic molecules with HF, DFT and MP2 using Gaussian 03. For MP2, I use the keywords "Density=MP2 Pop=Regular", and the output says that the MP2 density is used. The numbers for HF and MP2 are extremely close (at least 3 digits). Is this to be expected, or is there something I am missing?
>
> I assume a better way to get vertical excitation energies would be to calculate the first roots with CIS or TDDFT. Is this correct?
>
> Herbert>
>
>
From owner-chemistry@ccl.net Wed Aug 9 07:29:00 2006
From: "Michael Shokhen shokhen^^^mail.biu.ac.il" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: CCL SCRF solvation energy structure-additivity decomposition
Message-Id: <-32361-060809072531-30047-IpOVAZDRk4bD9b62xXC1Jw(a)server.ccl.net>
X-Original-From: "Michael Shokhen" <shokhen,+,mail.biu.ac.il>
Date: Wed, 9 Aug 2006 07:25:31 -0400
Sent to CCL by: "Michael Shokhen" [shokhen\a/mail.biu.ac.il]
Dear colleagues,
My question concerns a SCRF continuum solvation model
in frames of Poisson-Bolzmann equation implemented in quantum mechanical
calculations.
The molecular cluster, S (solute), solvated in a polar solvent can contain several charged groups. The total structure of solute, S, can be formally decomposed on substructures, s(i), where every s(i) contains only one charged group. In such a way the total solvation energy, Gsolv, in principle can be represented as a sum of contributions of
solvation energies, Gsolv(i), corresponding to solute substructures:
Gsolv = SUM[ Gsolv(i)] + B,
where B accounts all cross interactions to correct the additivity approximation.
I would appreciate, if somebody could address me to theoretical works
considering principal algorithms of such kind structure-additivity decomposition of the reaction field solvation energy.
All the best,
Michael
All the best,
Michael
From owner-chemistry@ccl.net Wed Aug 9 09:00:00 2006
From: "Andreas Klamt klamt()cosmologic.de" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: CCL SCRF solvation energy structure-additivity decomposition
Message-Id: <-32362-060809085606-25202-yaS/2tjI1lIOl7hYGCP5Qg[]server.ccl.net>
X-Original-From: Andreas Klamt <klamt|*|cosmologic.de>
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Date: Wed, 09 Aug 2006 14:55:58 +0200
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Sent to CCL by: Andreas Klamt [klamt- -cosmologic.de]
Dear Michael,
in some way my COSMO-RS method (see e.g. Klamt: COSMO-RS: From Quantum
Chemistry to Fluid Phase Thermodynamics and Drug Design, Elsevier 2005)
is using such kind of additivity. Starting from the solvation energy of
the molecules in a conductor all differences of the solvation energies
in real solvents to the conductor (and between different solvents) are
calculated as surface integrals, and hence each substructure s(i) would
thus contribute additive to the solvation free energy difference. Thus
differences of the solvation free energy between different solvents can
be considered as rather additive, but the solvation energy from the
vacuum to the conductor is much less additive, especially for charged
species. But most likely you are not interested in the charged species
in the gasphase or vacuum, but just in differences between diferent
solvents, right?
Andreas
Michael Shokhen shokhen^^^mail.biu.ac.il schrieb:
> Sent to CCL by: "Michael Shokhen" [shokhen\a/mail.biu.ac.il]
> Dear colleagues,
>
> My question concerns a SCRF continuum solvation model
> in frames of Poisson-Bolzmann equation implemented in quantum mechanical
> calculations.
>
> The molecular cluster, S (solute), solvated in a polar solvent can contain several charged groups. The total structure of solute, S, can be formally decomposed on substructures, s(i), where every s(i) contains only one charged group. In such a way the total solvation energy, Gsolv, in principle can be represented as a sum of contributions of
> solvation energies, Gsolv(i), corresponding to solute substructures:
>
>
> Gsolv = SUM[ Gsolv(i)] + B,
>
>
> where B accounts all cross interactions to correct the additivity approximation.
> I would appreciate, if somebody could address me to theoretical works
> considering principal algorithms of such kind structure-additivity decomposition of the reaction field solvation energy.
>
> All the best,
> Michael
>
> All the best,
>
> Michael>
>
>
>
>
>
--
-----------------------------------------------------------------------------
Dr. habil. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany
Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9
e-mail: klamt-*-cosmologic.de
web: www.cosmologic.de
-----------------------------------------------------------------------------
COSMOlogic
Your Competent Partner for
Computational Chemistry and Fluid Thermodynamics
-----------------------------------------------------------------------------
From owner-chemistry@ccl.net Wed Aug 9 09:55:00 2006
From: "Steve Gwaltney drg51^-^ra.msstate.edu" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL:G: MP2 HOMO-LUMO gap with G03
Message-Id: <-32363-060808220333-1414-i40jeT/OX3HJDJdG3YscMw(-)server.ccl.net>
X-Original-From: Steve Gwaltney <drg51_._ra.msstate.edu>
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Date: Tue, 8 Aug 2006 20:20:19 -0500 (CDT)
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Sent to CCL by: Steve Gwaltney [drg51 .. ra.msstate.edu]
On Tue, 8 Aug 2006, Herbert Fruchtl herbert.fruchtl*_*st-andrews.ac.uk wrote:
> Sent to CCL by: "Herbert Fruchtl" [herbert.fruchtl!^!st-andrews.ac.uk]
> Something I should probably know, but...
>
> I am calculating the HOMO-LUMO gap of small organic molecules with HF,
DFT and MP2 using Gaussian 03. For MP2, I use the keywords "Density=MP2
Pop=Regular", and the output says that the MP2 density is used. The
numbers for HF and MP2 are extremely close (at least 3 digits). Is this to
be expected, or is there something I am missing?
>
> I assume a better way to get vertical excitation energies would be to
calculate the first roots with CIS or TDDFT. Is this correct?
>
> Herbert
>
There appear to be a couple of misconceptions here. First, the HOMO-LUMO
gap has little to do with excitation energies. Specifically, the LUMO
calculated using most basis sets is not the "LUMO" most chemists think of.
This is especially true when using very diffuse basis sets, where the LUMO
often becomes an approximation to a free electron. Second, MP2 will not
change the orbital energies, since the orbital energies are the
eigenvalues of the Fock matrix.
If you want the vertical excitation energies, you need an excited state
method. For HF the corresponding method is CIS, which can have an error
of up to 2 eV. Just like with HF, CIS energies are bad, but the
geometries are decent. The corresponding method to DFT is TDDFT. This is
normally pretty reliable for excited states well below the first Rydberg
state. If you want an excited state method that corresponds to MP2, you
should use CIS(D).
Steve
Dr. Steven Gwaltney Phone: 662-325-7602
Assistant Professor Fax: 662-325-1618
Department of Chemistry, Mail: Box 9573
Center for Environmental Health Sciences, Mississippi State University
and HPCC Center for Computational Sciences ississippi State, MS 39762
From owner-chemistry@ccl.net Wed Aug 9 11:42:00 2006
From: "Eric Scerri scerri _ chem.ucla.edu" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Latest issue Foundations of Chemistry
Message-Id: <-32364-060808082329-9374-VQuVDNvbAkjrLb6/gfNpGA() server.ccl.net>
X-Original-From: "Eric Scerri" <scerri-x-chem.ucla.edu>
Date: Tue, 8 Aug 2006 10:54:14 -0000
Sent to CCL by: "Eric Scerri" [scerri=chem.ucla.edu]
FOUNDATIONS OF CHEMISTRY/ VOLUME 8 / NUMBER 1
Editorial 22 pp. 1 - 2
Eric Scerri
A Process Theory of Enzyme Catalytic Power � the Interplay of Science
and Metaphysics pp. 3 - 29
Ross L. Stein
Concerning the Position of Hydrogen in the Periodic Table pp. 31 - 35
Lawrence J. Sacks
The Role of Observables and Non-observables in Chemistry: A Critique of
Chemical Language pp. 37 - 52
Shant Shahbazian and Mansour Zahedi
Gestalt Switch in Molecular Image Perception: The Aesthetic Origin of
Molecular Nanotechnology in Supramolecular Chemistry pp. 53 - 72
Joachim Schummer
Ontological Reduction: A Comment on Lombardi and LaBarca pp. 73 - 80
Paul Needham
The ontological autonomy of the chemical world: a response to Needham
pp. 81 - 92
Olimpia Lombardi and Mart�n Labarca
--------------------------------------------------------------
THE PERIODIC TABLE: ITS STORY AND ITS SIGNIFICANCE, by Eric Scerri
Published by Oxford University Press on Sept 10th, 2006.
see OUP website or Amazon.com for placing advance orders.
--------------------------------------------------------
Dr. Eric Scerri,
Department of Chemistry and Biochemistry,
UCLA,
Los Angeles,
CA 90095,
UCLA web page,
http://chem.ucla.edu/dept/Faculty/scerri/index.html
Editor of Foundations of Chemistry,
http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882-
detailsPage%253Djournal%257
From owner-chemistry@ccl.net Wed Aug 9 15:31:01 2006
From: "Christian Pilger christian.pilger%a%gmx.net" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: CHIME string conversion
Message-Id: <-32365-060809152852-17222-P6w8PqPFoUYI0c9538dorQ%a%server.ccl.net>
X-Original-From: "Christian Pilger" <christian.pilger**gmx.net>
Date: Wed, 9 Aug 2006 15:28:52 -0400
Sent to CCL by: "Christian Pilger" [christian.pilger^^^gmx.net]
Dear CCLers,
are you aware of software allowing for the conversion of the MDL CHIME string format into something other like SMILES, Tripos-mol2, MDL-mol etc. ? I checked openbabel but it does not seem to be suited for this task.
Regards,
Christian