"CCL" <owner-chemistry-,-server.ccl.net>
"Labanowski, Jan -id#3pv-" <janl-,-theworld.com>
Message-Id: <ccl-m:28846-w:050707030502-14341-e:uNy46x+EILo1kNckC1/Z/g-id#3pv--,-server.ccl.net>
X-Original-From:Jan K Labanowski <jlabanow-,-nd.edu>
Sender: owner-chemistry-,-server.ccl.net
Errors-To: owner-chemistry-,-server.ccl.net
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
MIME-Version: 1.0
From: Jan K Labanowski <jlabanow-,-nd.edu>
--
Jan K. Labanowski, Ph.D. Tel. (574) 631-5465
Science Computing Facility FAX (574) 631-9293
University of Notre Dame
225 Nieuwland Science Hall
Notre Dame, IN 46556-5670
-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to: CHEMISTRY-,-ccl.net
Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST-,-ccl.net
HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
If your is mail bouncing from ccl.net domain due to spam filters, please
use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
From: "CCL" <owner-chemistry(_)server.ccl.net>
To: "Labanowski, Jan -id#3pv-" <janl(_)theworld.com>
Subject: CCL: Confirm: Fwd: Re: CCL: this is test <[050707054737-32691]>
Message-Id: <ccl28847-w050707064810-4871-e:uNy46x+EILo1kNckC1/Z/g-id#3pv(_)server.ccl.net>
Sent to CCL by: Jan K Labanowski <jlabanow(_)nd.edu>
Sender: owner-chemistry(_)server.ccl.net
Errors-To: owner-chemistry(_)server.ccl.net
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1
MIME-Version: 1.0
Sent to CCL by: Jan K Labanowski <jlabanow(_)nd.edu>
--
Jan K. Labanowski, Ph.D. Tel. (574) 631-5465
Science Computing Facility FAX (574) 631-9293
University of Notre Dame
225 Nieuwland Science Hall
Notre Dame, IN 46556-5670
----- Forwarded message from CCL Confirmation Request <confirmation(_)ccl.net> -----
Date: Thu, 7 Jul 2005 05:47:37 -0400
From: CCL Confirmation Request <confirmation(_)ccl.net>
Reply-To: CCL Confirmation Request <confirmation(_)ccl.net>
Subject: Confirm: Fwd: Re: CCL: this is test <[050707054737-32691]>
To: jlabanow(_)nd.edu
[This is an automatically generated message]
Dear jlabanow(_)nd.edu
This is a request to confirm that you recently sent a message
to Computational Chemistry List (CCL) with a subject:
Fwd: Re: CCL: this is test
If this was indeed you, please click on one of the links
below (or cut/paste it in your browser). Your message
will not be sent without your action.
Please view the source of your message as we received it
and then decide if you want to send the message to CCL:
http://www.ccl.net/cgi-bin/ccl/vm?m=050707054737-32691
You can authorize distribution of your message either
on the Web form given above or by replaying to this message.
Just click on the Reply option in your e-mail viewing
program, but please do not modify the text of the message.
If you posted to CCL before, your message will be distributed
without delay. If this is the first submission from your address
the message will have to be reviewed by CCL administrators before
it is send.
If you do not see your message processed within a day or two,
please remind us at:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=========== What the hack is this mail? ==============
If it was not you who sent the message, please read further
for explanations.
If you are surprised with this message and it was not you
who sent the message to CCL, then someone wanted to impersonate
you and he/she entered your e-mail address on the From: line or
on a Web fom. Unfortunately spammers commonly do that and there
is no easy way to prevent it. You can view the message source
and its header information (Received: lines) at:
http://www.ccl.net/cgi-bin/ccl/vm-ns?m=050707054737-32691
to get a clue how it got to us.
If you are not associated with CCL and you want to prevent
any future messages like this from our server, please click
on the link below:
http://www.ccl.net/cgi-bin/ccl/do-not-accept?r=050707054737-32691
It will place your address on the list that is looked up
before automatic confirmation messages are sent.
If you are a CCL subscriber, this will not affect your
subscription to CCL, however, your messages will have
to be reviewed by CCL administrators before they are
distributed.
Thank you for your cooperation
CCL Administrators
E-mail: chemistry-request(_)ccl.net
http://www.ccl.net
----- End forwarded message -----
-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to: CHEMISTRY(_)ccl.net
Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST(_)ccl.net
HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
If your is mail bouncing from ccl.net domain due to spam filters, please
use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
From chemistry-request@ccl.net Thu Jul 7 23:45:44 2005
Received: from mercury.chem.pitt.edu (mercury.chem.pitt.edu [136.142.60.100])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j683jhoD000581
for <chemistry ## ccl.net>; Thu, 7 Jul 2005 23:45:43 -0400
Received: from ringo.chem.pitt.edu (localhost.localdomain [127.0.0.1])
by mercury.chem.pitt.edu (Postfix) with SMTP id DB9A04840
for <chemistry ## ccl.net>; Thu, 7 Jul 2005 23:32:46 -0400 (EDT)
Received: from 200.165.141.250
(SquirrelMail authenticated user gustavo)
by mercury.chem.pitt.edu with HTTP;
Thu, 7 Jul 2005 23:32:46 -0400 (EDT)
Message-ID: <2689.200.165.141.250.1120793566.squirrel ## mercury.chem.pitt.edu>
Date: Thu, 7 Jul 2005 23:32:46 -0400 (EDT)
Subject: Symmetry breaking during CASSCF
From: <gustavo ## mercury.chem.pitt.edu>
To: <chemistry ## ccl.net>
X-Priority: 3
Importance: Normal
X-Mailer: SquirrelMail (version 1.2.11)
MIME-Version: 1.0
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit
X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Dear CCL Readers,
I have a planar conjugated organic molecule that, on paper, has D2h
symmetry. I am working with the hypothesis that the molecule is a
biradical singlet. I want to perform a CASSCF(2,2) on this molecule
to estimate the biradical character of this molecule. When I
calculate the molecule with the constraint that the molecule has D2h
symmetry, the calculation has severe convergence problems. If I
remove this constraint, the molecule distorts to a C2v symmetry and I
obtain a biradical character ~20%. I checked the orbitals being used
for the CASSCF calculation and they look right (one nonbonding and
another slightly antibonding).
Is the situation described above correct? Can an organic molecule
have such a symmetry breaking as a result of a CASSCF calculation? Is
the molecule really a C2v system? Any suggestions are welcome.
Thank you very much in advance for your help.
Sincerely yours,
Gustavo L.C. Moura
gustavo ## mercury.chem.pitt.edu
From chemistry-request@ccl.net Thu Jul 7 21:39:02 2005
Received: from rozz.csail.mit.edu (rozz.csail.mit.edu [128.30.2.16])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j681d0vT027121
for <chemistry !! ccl.net>; Thu, 7 Jul 2005 21:39:00 -0400
Received: from pool-70-19-174-107.bos.east.verizon.net ([70.19.174.107] helo=[192.168.2.100])
by rozz.csail.mit.edu with esmtpsa (TLSv1:RC4-MD5:128)
(Exim 4.50)
id 1Dqgjc-00049s-Pg
for chemistry !! ccl.net; Thu, 07 Jul 2005 20:28:53 -0400
Message-ID: <42CDC8C1.3040206 !! mit.edu>
Date: Thu, 07 Jul 2005 20:28:49 -0400
From: "David F. Green" <dfgreen !! mit.edu>
User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317)
X-Accept-Language: en-us, en
MIME-Version: 1.0
To: chemistry !! ccl.net
Subject: Re: CCL: W:Solvation free energy for aromatic hydrocarbon
References: <200507072007.j67K7coC007174 !! server.ccl.net>
In-Reply-To: <200507072007.j67K7coC007174 !! server.ccl.net>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Aromatic systems are weakly polar. Certainly, compared to other groups
in proteins --- hydroxyls, amides, carboxylic acids, amines and so on
--- they are relatively hydrophobic. However, they are significantly
more polar than aliphatic hydrocarbons. As you pointed out, this is
borne out by the free energies of hydration, as well as by theoretical
studies. However, the interior of a protein is a vacuum, and is not
even entirely hydrophobic (at minimum, there are buried back-bone
amides). Looking at transfer between water and octanol (a moderately
non-polar enviroment), benzene falls out somwhere between propane and
butane --- certainly preferring the more hydrophobic environment. This
all works out as a result of the balancing of enthalpic (both
electrostatic and van der Waals, in molecular mechanics' terms)
interactions between the solute and solvent and entropic terms resulting
> from solvent structure. More statistical frameworks (like
hydrophobicity scales and the like) are really just capturing the same
underlying physics, which is why you'll often here people refering to
them in the same language (e.g. the hydrophobic effect).
To give a quick example of how the vacuum to water transfer free energy
may be negative, while the hydrophobic solvent to water transfer energy
may be positive, just think about van der Waals interactions; there are
none in vacuum, and plenty between an aromatic system in hydrophobic
solvent. The weak dielectric response of hydrophobic solvents (around 2
at the very minimum) gives an added bonus, and as always, entropy is a
hard one to deal with perfectly.
But in a nutshell, aromatic certainly do have favorable hydration free
energies despite generally considered "hydrophobic". It's not a
misnomer, but more a difference in reference state. Of course, every
thing is always a little more complicated than what anyone tells you,
but that's what makes it all fun.
+--------------------------------------------------------------------+
| David F. Green | |
| Postdoctoral Associate | Office: 617-253-5438 |
| Division of Bioengineering and Computer | Mobile: 617-953-3922 |
| Science & Artificial Intelligence Lab | Fax: 617-252-1816 |
| Massachusetts Institute of Technology | |
| 32 Vassar St., 32-211 | E-mail: dfgreen !! mit.edu |
| Cambridge, MA 02139 | |
+--------------------------------------------------------------------+
Chemical, , Bond wrote:
> Hi there,
>
> I am confused with a single concept: what should be the sign for the solvation free energy for a fragment like phenyl?
>
> There are many experimental data of solvation free energy for aromatic hydrocarbons, such as benzene, naphthalene, etc, but they are all negative surprisingly. I looked at several papers with models of solvation energy, and their predictions all all have negative solvation energies for those compounds, just like the experiments.
>
> Typically when a phenyl group is transfered from water into protein, we would like to say there is a negative(beneficial) desolvation energy, or the usual called hydrophobic effect. And this has been used in tons of models for protein simulation or protein-ligand binding. Note, in this context, the solvation energy (from gas into water) is positive!
>
> Is there something wrong over here? Or just some artifact from the fitting?
>
> Hope there would be some good comments.
>
> Thanks a lot,
> Bond
>
>
> -= This is automatically added to each message by the mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
> and send your message to: CHEMISTRY _()_ ccl.net
>
> Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST _()_ ccl.net
> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
>
> If your is mail bouncing from ccl.net domain due to spam filters, please
> use the Web based form from CCL Home Page
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>
>
>
>
>
From chemistry-request@ccl.net Fri Jul 8 01:33:33 2005
Received: from mrbusi1.netcologne.de (mrbusi1.netcologne.de [194.8.194.213])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j685XTsW005614
for <chemistry _()_ ccl.net>; Fri, 8 Jul 2005 01:33:30 -0400
Received: from cosmologic.de (xdsl-213-196-241-161.netcologne.de [213.196.241.161])
by mrbusi1.netcologne.de (Postfix) with ESMTP id 483F01A0028
for <chemistry _()_ ccl.net>; Fri, 8 Jul 2005 07:33:27 +0200 (CEST)
Message-ID: <42CE1025.8080803 _()_ cosmologic.de>
Date: Fri, 08 Jul 2005 07:33:25 +0200
From: Andreas Klamt <klamt _()_ cosmologic.de>
User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4
X-Accept-Language: en-us, en
MIME-Version: 1.0
To: chemistry _()_ ccl.net
Subject: Re: CCL: W:Solvation free energy for aromatic hydrocarbon
References: <200507072007.j67K7coC007174 _()_ server.ccl.net>
In-Reply-To: <200507072007.j67K7coC007174 _()_ server.ccl.net>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 7bit
X-Spam-Status: No, score=1.1 required=5.0 tests=FORGED_RCVD_HELO,
RCVD_IN_NJABL_PROXY autolearn=no version=3.0.4
X-Spam-Level: *
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Hi Bond,
the concepts of the solavtion models are right. You must take into
account the van der Waals (vdW) energies, which to first order can be
considered as a kind of vdWs surface energy.
More or less accidentally, for water vdWs energy and surface tension
(cavity formation free energy) almost cancel, so that hydration free
energies of alkanes are very slightly positive. Since aromatics (due to
the quadrupole moment) are slightly more polar than alkanes, hydration
free energies of aromatics are slightly negative, as you say.
In a less polar solvent than water the cavitation free energy is much
less positive (typically close to zero). Thus the solavtion free energy
in such solvent would be much more negative that it is into water, and
thus the ballance of the transfer of aromatics from water to less polar
solvents is much in favor of the non-polar solvent.
You can study these terms in detail in our solvation model COSMO-RS (see
www.cosmologic.de).
Regards
Andreas
Chemical, , Bond wrote:
>Hi there,
>
>I am confused with a single concept: what should be the sign for the solvation free energy for a fragment like phenyl?
>
>There are many experimental data of solvation free energy for aromatic hydrocarbons, such as benzene, naphthalene, etc, but they are all negative surprisingly. I looked at several papers with models of solvation energy, and their predictions all all have negative solvation energies for those compounds, just like the experiments.
>
>Typically when a phenyl group is transfered from water into protein, we would like to say there is a negative(beneficial) desolvation energy, or the usual called hydrophobic effect. And this has been used in tons of models for protein simulation or protein-ligand binding. Note, in this context, the solvation energy (from gas into water) is positive!
>
>Is there something wrong over here? Or just some artifact from the fitting?
>
>Hope there would be some good comments.
>
>Thanks a lot,
>Bond
>
>
>-= This is automatically added to each message by the mailing script =-
>To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
>and send your message to: CHEMISTRY _()_ ccl.net
>
>Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST _()_ ccl.net
>HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
>
>If your is mail bouncing from ccl.net domain due to spam filters, please
>use the Web based form from CCL Home Page
>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>
>
>
>
>
>
>
>
>
--
-----------------------------------------------------------------------------
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 chemistry-request@ccl.net Fri Jul 8 05:28:04 2005
Received: from hermes1.cf.ac.uk (hermes1.cf.ac.uk [131.251.0.112])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j689S1Bm019982
for <chemistry _()_ ccl.net>; Fri, 8 Jul 2005 05:28:02 -0400
Received: from maincf1p.cf.ac.uk ([131.251.4.20])
by hermes1.cf.ac.uk with esmtp (Exim 4.34)
id 1Dqo4u-0002qk-TV
for chemistry _()_ ccl.net; Fri, 08 Jul 2005 09:19:20 +0100
Received: from Cardiff_University-MTA by MAINCF1P.cf.ac.uk
with Novell_GroupWise; Fri, 08 Jul 2005 09:19:20 +0100
Message-Id: <s2ce4518.045 _()_ MAINCF1P.cf.ac.uk>
X-Mailer: Novell GroupWise Internet Agent 6.5.4
Date: Fri, 08 Jul 2005 09:19:13 +0100
From: "Jamie Platts" <platts _()_ Cardiff.ac.uk>
To: <chemistry _()_ ccl.net>
Subject: Re: CCL: MP2 virial value
Mime-Version: 1.0
Content-Type: text/plain; charset=US-ASCII
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
X-Virus-Scanned: Cardiff University Sophos AV
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Dear Pasikonik
You can obtain the virial value from -V/T = 1 - E/T. Both are reported by
Gaussian,
the energy as EUMP2 (or just MP2 in the archive summary), and the kinetic
energy
as KE, just below the multipole information. Make sure you use the "density"
keyword
or you'll probably get the HF value for KE.
As an example, values for Cl2 using MP2/6-311G* are
EUMP2 = -0.91923578058246D+03
KE= 9.195031259365D+02
-V/T = 1.99971
Hope this helps,
Jamie
----------------------------------------------------------
Jamie Platts
School of Chemistry Phone: +44 (0) 2920 874950
Cardiff University Email: platts _()_ cf.ac.uk
Park Place FAX: +44 (0) 2920 874030
Cardiff CF10 3AT www.cf.ac.uk/chemy
>>> drpasikonik _()_ yahoo.com 07/07/05 11:56 pm >>>
Hi everybody
Can anybody tell me how to obtain the virial (-V/T) value for the MP2
calculations in Gaussian?
There is no problem on the HF or DFT level, but this property is not listed for
MP2. How can I print it
Thank you in advance
Pasikonik
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
From chemistry-request@ccl.net Fri Jul 8 10:47:44 2005
Received: from mail-gw4.njit.edu (mail-gw4.njit.edu [128.235.251.32])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68ElfST000849
for <chemistry _()_ ccl.net>; Fri, 8 Jul 2005 10:47:41 -0400
Received: from webmail.njit.edu (webmail.njit.edu [128.235.251.121])
by mail-gw4.njit.edu (8.12.10/8.12.4) with ESMTP id j68DwvSt009948;
Fri, 8 Jul 2005 09:58:57 -0400 (EDT)
Received: (from apache@localhost)
by webmail.njit.edu (8.11.7p1+Sun/8.11.7) id j68DwuR00363;
Fri, 8 Jul 2005 09:58:56 -0400 (EDT)
To: chemistry _()_ ccl.net, mclaro2727 _()_ yahoo.com
Subject: Re: CCL: 3D to chemical name
Message-ID: <1120831136.42ce86a06b781 _()_ webmail.njit.edu>
Date: Fri, 08 Jul 2005 09:58:56 -0400 (EDT)
From: dnp5 _()_ njit.edu
References: <4F7EC9B21FB40043A33952CF23582FE903C89823 _()_ EXCHANGE.camsoft.com>
In-Reply-To: <4F7EC9B21FB40043A33952CF23582FE903C89823 _()_ EXCHANGE.camsoft.com>
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit
User-Agent: IMP/PHP IMAP webmail program 2.2.4
X-Originating-IP: 196.3.51.241
X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Hi Claro:
You can try ACD/ChemSketch 8.0 Freeware from the link below.
http://www.acdlabs.com/download/chemsk.html
Deepangi
Quoting Tony Yuan <TYuan _()_ cambridgesoft.com>:
>
>
> Try ChemDraw. It can do 3D => 2D => Chemical Name.
> Also try ChemFinder.com and ChemACX.com, you can search suppliers by
> doing structure query.
> Chem3D can convert PDB files to MDL mol files and CDX files.
>
> Good luck!
>
> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request _()_ ccl.net]
> On
> Behalf Of Noel O'Boyle
> Sent: Thursday, July 07, 2005 4:01 AM
> To: chemistry _()_ ccl.net
> Cc: mclaro2727 _()_ yahoo.com
> Subject: CCL: 3D to chemical name
> Importance: Low
>
> Dear Claro,
>
> Many chemical don't have simple names, and many suppliers use
> different
> names
> for the same chemical. What you need is the supplier code for the
> chemical.
> It is sometimes possible (for example, on the sigma-aldrich webpage)
> to
> search
> the supplier's catalogue using the chemical formula, or by drawing the
> molecule
> on the web page.
>
> A note of warning: often the ligand structures taken from pdb files
> contain
> just the carbon skeleton, and are missing protons and bond orders.
> Just
> to
> make your life easier :-)
>
> Regards,
> Noel O'Boyle.
>
> >-- Original Message --
> >Date: Wed, 6 Jul 2005 13:33:44 -0700 (PDT)
> >From: michelle claro <mclaro2727 _()_ yahoo.com>
> >Subject: CCL: 3D to chemical name
> >To: chemistry _()_ ccl.net
> >Reply-To: chemistry _()_ ccl.net
> >
> >
> >Hello,
> >
> >I have about 50 pdb structures (no protein in the pdb just the
> ligand)
> but
> >I need the chemical names in order to purchase them. What is the
> easiest
> >way to get a chemical name from a pdb? Thanks in advance.
> >
> >M. Claro
> >
> >
> >__________________________________________________
> >Do You Yahoo!?
> >Tired of spam? Yahoo! Mail has the best spam protection around
> >http://mail.yahoo.com
>
>
>
>
>
> To send e-mail to subscribers of CCL put the string CCL: on your
> Subject: line
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST _()_ ccl.net
>
>
>
>
>
>
>
>
> -= This is automatically added to each message by the mailing script
> =-
> To send e-mail to subscribers of CCL put the string CCL: on your
> Subject: line
> and send your message to: CHEMISTRY _()_ ccl.net
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST _()_ ccl.net
> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
>
> If your is mail bouncing from ccl.net domain due to spam filters,
> please
> use the Web based form from CCL Home Page
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>
>
>
>
>
>
From chemistry-request@ccl.net Fri Jul 8 09:18:02 2005
Received: from fallback0.mail.ox.ac.uk (fallback0.mail.ox.ac.uk [129.67.1.175])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68DHw9k029520
for <chemistry _()_ ccl.net>; Fri, 8 Jul 2005 09:17:59 -0400
Received: from relay0.mail.ox.ac.uk ([129.67.1.161])
by fallback0.mail.ox.ac.uk with esmtp (Exim 4.43)
id 1Dqrei-0003Xm-Og
for chemistry _()_ ccl.net; Fri, 08 Jul 2005 13:08:32 +0100
Received: from smtp2.herald.ox.ac.uk ([163.1.0.235])
by relay0.mail.ox.ac.uk with esmtp (Exim 4.50)
id 1Dqreh-0006At-1a
for chemistry _()_ ccl.net; Fri, 08 Jul 2005 13:08:31 +0100
Received: from webmail223.herald.ox.ac.uk ([163.1.0.223])
by smtp2.herald.ox.ac.uk with esmtp (Exim 3.35 #1)
id 1Dqreh-0004Li-3n
for chemistry _()_ ccl.net; Fri, 08 Jul 2005 13:08:31 +0100
Received: by webmail223.herald.ox.ac.uk (Postfix, from userid 101)
id F16112A07C; Fri, 8 Jul 2005 13:08:30 +0100 (BST)
Content-Type: text/plain
Content-Disposition: inline
Content-Transfer-Encoding: binary
MIME-Version: 1.0
X-Mailer: MIME-tools 5.411 (Entity 5.404)
From: Yvette Sturdy <yvette.sturdy _()_ chemistry.oxford.ac.uk>
Date: Fri, 8 Jul 2005 13:08:30 +0100 (BST)
To: chemistry _()_ ccl.net
Subject: Wilson B Matrix
X-Webmail-Originating-Ip: 129.67.105.161
X-Webmail-Sender: exet0842
Message-Id: <20050708120830.F16112A07C _()_ webmail223.herald.ox.ac.uk>
X-Spam-Status: No, score=0.5 required=5.0 tests=DNS_FROM_RFC_WHOIS
autolearn=no version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Dear All,
I'm having some problems obtaining the Wilson B matrix.
I have outputted it from Gamess. The package calculates the z matrix from
the cartesians correctly, but if i take the B matrix it gives and pre-multiply
the cartesians only the bond lengths come out correctly. Has anyone had
any experience with this? Or does anyone know of a code i can use to obtain
the B matrix?
(I've tried with gaussian98 and encounter similar problems)
Thanks.
Yvette.
--
Yvette Sturdy
Physical and Theoretical Chemistry Laboratory
University of Oxford
From chemistry-request@ccl.net Fri Jul 8 07:34:45 2005
Received: from server.ccl.net (ccl [127.0.0.1])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68BYi8O026034
for <chemistry _()_ ccl.net>; Fri, 8 Jul 2005 07:34:44 -0400
Received: (from apache@localhost)
by server.ccl.net (8.13.1/8.13.1/Submit) id j68BYinl026033
for chemistry _()_ ccl.net; Fri, 8 Jul 2005 07:34:44 -0400
Date: Fri, 8 Jul 2005 07:34:44 -0400
Message-Id: <200507081134.j68BYinl026033 _()_ server.ccl.net>
X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request _()_ ccl.net using -f
From: "Gustavo, L.C., Moura" <gustavo _()_ mercury.chem.pitt.edu>
To: chemistry _()_ ccl.net
X-Web-Message-Number: 050708073319-25962
Subject: W:Symmetry breaking during CASSCF
X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Dear CCL Readers,
I have a planar conjugated organic molecule that, on paper, has D2h
symmetry. I am working with the hypothesis that the molecule is a
biradical singlet. I want to perform a CASSCF(2,2) on this molecule
to estimate the biradical character of this molecule. When I
calculate the molecule with the constraint that the molecule has D2h
symmetry, the calculation has severe convergence problems. If I
remove this constraint, the molecule distorts to a C2v symmetry and I
obtain a biradical character ~20%. I checked the orbitals being used
for the CASSCF calculation and they look right (one nonbonding and
another slightly antibonding).
Is the situation described above correct? Can an organic molecule
have such a symmetry breaking as a result of a CASSCF calculation? Is
the molecule really a C2v system? Any suggestions are welcome.
Thank you very much in advance for your help.
Sincerely yours,
Gustavo L.C. Moura
gustavo _()_ mercury.chem.pitt.edu
From chemistry-request@ccl.net Fri Jul 8 05:13:23 2005
Received: from distrib2.mail.u-psud.fr (distrib2.mail.u-psud.fr [129.175.34.154])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j689DJml019379
for <chemistry !! ccl.net>; Fri, 8 Jul 2005 05:13:20 -0400
Received: from intfiltre3.mail.u-psud.fr (intfiltre3.mail.u-psud.fr [129.175.34.151])
by distrib2.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j689DE04018574
for <chemistry !! ccl.net>; Fri, 8 Jul 2005 11:13:14 +0200
Received: from post1.mail.u-psud.fr (post1.mail.u-psud.fr [129.175.34.87])
by intfiltre3.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j689Ct80005378
for <chemistry !! ccl.net>; Fri, 8 Jul 2005 11:13:13 +0200
Received: from ext.lcp.u-psud.fr (ext.lcp.u-psud.fr [129.175.100.5])
by post1.mail.u-psud.fr (8.12.10/8.12.0.Beta10) with ESMTP id j689B6u3027585
for <chemistry !! ccl.net>; Fri, 8 Jul 2005 11:11:07 +0200
Received: from lcp.u-psud.fr (pc7.lcp.u-psud.fr [129.175.101.37])
by ext.lcp.u-psud.fr (8.13.1/8.13.1) with ESMTP id j689B9FE011409
for <chemistry !! ccl.net>; Fri, 8 Jul 2005 11:11:10 +0200
Message-ID: <42CE432D.2010104 !! lcp.u-psud.fr>
Date: Fri, 08 Jul 2005 11:11:09 +0200
From: Pierre Archirel <pierre.archirel !! lcp.u-psud.fr>
User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr; rv:1.4.1) Gecko/20031114
X-Accept-Language: fr, en
MIME-Version: 1.0
To: chemistry !! ccl.net
Subject: CCL: dissociation problem
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: 8bit
X-Scanned: by amavis
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Dear Elmar,
I would say the issue you are refering to has nothing to do with PCM,
but is probably due to a DFT artifact, which is the wrong dissociation
of NaCl, even in the gas phase. Your asymptotic system is a singlet open
shell,
with two electrons, alone in their orbitals. DFT poorly addresses this
situation,
because of the approximative cancelation of the self interaction.
To check this:
1- verify that at the crude HF level, your long range PCM energy is the sum
of the PCM energies of the fragments.
2- check if your (gas phase) long range B3LYP calculation yields
fragments with 0 charges. If not, DFT is of no help to you.
P.
__________________________________________________________
Pierre Archirel
Groupe de Chimie Thiorique
Laboratoire de Chimie Physique Tel: 01 69 15 63 86
Bat 349 Fax: 01 69 15 61 88
91405 Orsay Cedex
France pierre.archirel !! lcp.u-psud.fr
__________________________________________________________
From chemistry-request@ccl.net Fri Jul 8 00:13:51 2005
Received: from chem.umn.edu (chemsun.chem.umn.edu [128.101.157.2])
by server.ccl.net (8.13.1/8.13.1) with SMTP id j684Dko5001958
for <CHEMISTRY ## ccl.net>; Fri, 8 Jul 2005 00:13:47 -0400
Received: (qmail 2101 invoked from network); 8 Jul 2005 03:13:44 -0000
Received: from unknown (HELO ?10.0.1.2?) (134.84.5.63)
by 0 with SMTP; 8 Jul 2005 03:13:44 -0000
Mime-Version: 1.0 (Apple Message framework v622)
Content-Type: multipart/alternative; boundary=Apple-Mail-1-751306894
Message-Id: <452bfca9f0024f1b3c7e931d0d8a8047 ## chem.umn.edu>
Cc: CHEMISTRY ## ccl.net
From: Christopher Cramer <cramer ## chem.umn.edu>
Subject: Fwd: CCL: dissociation problem in PCM model ?
Date: Thu, 7 Jul 2005 22:13:47 -0500
To: Elmar Gerwalin <elg ## chemie.uni-kl.de>
X-Mailer: Apple Mail (2.622)
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
--Apple-Mail-1-751306894
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset=US-ASCII;
delsp=yes;
format=flowed
Elmar,
My textbook, Essentials of Computational Chemistry, actually has a
specific section (11.4.4 Potentials of Mean Force and Solvent
Structure) that mentions your problem. The issue is that continuum
models like the PCM variants involve the definition of a solute cavity,
typically defined as roughly the union of a set of van der Waals
spheres on all of the atoms. If you pull your solute apart, breaking a
bond, at some point you will exceed van der Waals contact and the poor
program has to decide what to do. It is quite unpleasant to solve the
Poisson equation with two cavities in a dielectric continuum... If
memory serves, PCM leaves some sort of neck between the two for awhile,
so that there is still a single cavity, but this clearly soon becomes a
bad approximation, since there is really solvent there. At some point,
the program probably just delivers an error message (and a cryptic one,
too, no doubt).
But, if you compute the separated species individually, then there
is no problem at all. Each has a well defined cavity and is infinitely
far from anything but solvent. The two calculations will not agree,
since the cavities were defined very differently.
The only widely used continuum model that does NOT suffer from this
discontinuity in a potential of mean force owing to cavity separation
is the Generalized Born model, which takes atomic radii as inputs but
does not use them to construct a formal cavity and is smooth and
continuous over all distances.
If you would like to try a GB model, you are welcome to employ one
of our SMx solvation models, freely available in a variety of codes,
including SMxGAUSS, which can either read a Gaussian output file as
input and run as a stand-alone code, or can be driven by G03 using the
"external" keyword. See comp.chem.umn.edu/mccdir/software.htm for full
details.
Best regards,
Chris
Begin forwarded message:
> From: Elmar Gerwalin <elg !! chemie.uni-kl.de>
> Date: July 7, 2005 3:29:35 PM CDT
> To: CHEMISTRY !! ccl.net
> Subject: CCL: dissociation problem in PCM model ?
> Reply-To: chemistry !! ccl.net
>
> Hi,
>
> I'm trying to describe dissociation processes in some small organic
> molecules.
> Therefore, I'm using B3LYP+SCRF(C-PCM, solvent=methanol) single point
> jobs to get the
> solvation energy at each step. Finally, a potential energy curve E(R)
> is my goal.
> R is the bond distance I'm interested in; e.g. a C-O, C-Cl bond or ,
> for testing purposes
> Na-Cl.
>
> But, unfortunately, wrong asymptotic behaviour (like a "size
> inconsistency problem") is
> observed in all cases: the "supermolecule's" solvation energy at large
> distances (10 or 20 A)
> is differing about more than 20 kcal/mole from the sum of the
> solvation energies of the two ions.
>
> My question is: is the problem known (references ?)? How can be it be
> accounted for ?
> Do I have to use specific energy terms given in gaussian's output
> and/or male a correction to them ?
>
> Any help is appreciated.
>
> Bye,
>
> Yours,
> Elmar
>
>
> --
> ========================================================
> Elmar Gerwalin , University of Kaiserslautern,Germany
> Dept. of Theoretical Chemistry
> elg !! chemie.uni-kl.de
> ========================================================
>
>
> -= This is automatically added to each message by the mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your
> Subject: line
> and send your message to: CHEMISTRY !! ccl.net
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST !! ccl.net
> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
>
> If your is mail bouncing from ccl.net domain due to spam filters,
> please
> use the Web based form from CCL Home Page
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
> +-+
>
>
>
>
>
>
--
Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone: (612) 624-0859 || FAX: (612) 626-2006
Mobile: (612) 597-5275
cramer !! pollux.chem.umn.edu
http://pollux.chem.umn.edu/~cramer
(website includes information about the textbook "Essentials
of Computational Chemistry: Theories and Models, 2nd Edition")
--Apple-Mail-1-751306894
Content-Transfer-Encoding: 7bit
Content-Type: text/enriched;
charset=US-ASCII
Elmar,
My textbook, Essentials of Computational Chemistry, actually has a
specific section (11.4.4 Potentials of Mean Force and Solvent
Structure) that mentions your problem. The issue is that continuum
models like the PCM variants involve the definition of a solute
cavity, typically defined as roughly the union of a set of van der
Waals spheres on all of the atoms. If you pull your solute apart,
breaking a bond, at some point you will exceed van der Waals contact
and the poor program has to decide what to do. It is quite unpleasant
to solve the Poisson equation with two cavities in a dielectric
continuum... If memory serves, PCM leaves some sort of neck between
the two for awhile, so that there is still a single cavity, but this
clearly soon becomes a bad approximation, since there is really
solvent there. At some point, the program probably just delivers an
error message (and a cryptic one, too, no doubt).
But, if you compute the separated species individually, then there
is no problem at all. Each has a well defined cavity and is infinitely
far from anything but solvent. The two calculations will not agree,
since the cavities were defined very differently.
The only widely used continuum model that does NOT suffer from this
discontinuity in a potential of mean force owing to cavity separation
is the Generalized Born model, which takes atomic radii as inputs but
does not use them to construct a formal cavity and is smooth and
continuous over all distances.
If you would like to try a GB model, you are welcome to employ one
of our SMx solvation models, freely available in a variety of codes,
including SMxGAUSS, which can either read a Gaussian output file as
input and run as a stand-alone code, or can be driven by G03 using the
"external" keyword. See comp.chem.umn.edu/mccdir/software.htm for full
details.
Best regards,
Chris
Begin forwarded message:
<excerpt><bold><color><param>0000,0000,0000</param>From:
</color></bold>Elmar Gerwalin <<elg !! chemie.uni-kl.de>
<bold><color><param>0000,0000,0000</param>Date: </color></bold>July 7,
2005 3:29:35 PM CDT
<bold><color><param>0000,0000,0000</param>To:
</color></bold>CHEMISTRY !! ccl.net
<bold><color><param>0000,0000,0000</param>Subject: </color>CCL:
dissociation problem in PCM model ?
<color><param>0000,0000,0000</param>Reply-To:
</color></bold>chemistry !! ccl.net
Hi,
I'm trying to describe dissociation processes in some small organic
molecules.
Therefore, I'm using B3LYP+SCRF(C-PCM, solvent=methanol) single point
jobs to get the
solvation energy at each step. Finally, a potential energy curve E(R)
is my goal.
R is the bond distance I'm interested in; e.g. a C-O, C-Cl bond or ,
for testing purposes
Na-Cl.
But, unfortunately, wrong asymptotic behaviour (like a "size
inconsistency problem") is
observed in all cases: the "supermolecule's" solvation energy at large
distances (10 or 20 A)
is differing about more than 20 kcal/mole from the sum of the
solvation energies of the two ions.
My question is: is the problem known (references ?)? How can be it be
accounted for ?
Do I have to use specific energy terms given in gaussian's output
and/or male a correction to them ?
Any help is appreciated.
Bye,
Yours,
Elmar
--
========================================================
Elmar Gerwalin , University of Kaiserslautern,Germany
Dept. of Theoretical Chemistry
elg !! chemie.uni-kl.de
========================================================
-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your
Subject: line
and send your message to: CHEMISTRY !! ccl.net
Send your subscription/unsubscription requests to:
CHEMISTRY-REQUEST !! ccl.net
HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
If your is mail bouncing from ccl.net domain due to spam filters,
please
use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
</excerpt>--
Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone: (612) 624-0859 || FAX: (612) 626-2006
Mobile: (612) 597-5275
cramer !! pollux.chem.umn.edu
http://pollux.chem.umn.edu/~cramer
(website includes information about the textbook "Essentials
of Computational Chemistry: Theories and Models, 2nd Edition")
--Apple-Mail-1-751306894--
From chemistry-request@ccl.net Thu Jul 7 22:47:31 2005
Received: from pantheon-po06.its.yale.edu (pantheon-po06.its.yale.edu [130.132.50.36])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j682lUR6030478
for <chemistry !! ccl.net>; Thu, 7 Jul 2005 22:47:30 -0400
Received: from yale.edu (patre.chem.yale.edu [128.36.107.41])
by pantheon-po06.its.yale.edu (8.12.11/8.12.11) with ESMTP id j681up27003813
for <chemistry !! ccl.net>; Thu, 7 Jul 2005 21:56:51 -0400
Message-ID: <42CDDC5D.30308 !! yale.edu>
Date: Thu, 07 Jul 2005 21:52:29 -0400
From: Jose Gascon <jose.gascon !! yale.edu>
User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1
X-Accept-Language: en-us, en
MIME-Version: 1.0
To: chemistry !! ccl.net
Subject: Re: CCL: dissociation problem in PCM model ?
References: <20050707202935.GA10202 !! pc1.chemie.uni-kl.de>
In-Reply-To: <20050707202935.GA10202 !! pc1.chemie.uni-kl.de>
Content-Type: text/plain; charset=us-ascii; format=flowed
Content-Transfer-Encoding: 7bit
X-YaleITSMailFilter: Version 1.2b (attachment(s) not renamed)
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Elmar, as I understand, DFT cannot be used to calculate dissociation
energies.
Consider just the case of H2+ (the most trivial molecule). Here you will get
the wrong assimptotic value. In fact Hartree-Fock will give you the
exact answer.
This is an intrinsic problem given by the fact that the density
functionals are not
known exactly. In the case of H2+ this results in an electron that can
literally interact
with itself.
My suggestion is to use MP2 or QCISD if you can afford it.
Best, jose
Elmar Gerwalin wrote:
>Hi,
>
>I'm trying to describe dissociation processes in some small organic molecules.
>Therefore, I'm using B3LYP+SCRF(C-PCM, solvent=methanol) single point jobs to get the
>solvation energy at each step. Finally, a potential energy curve E(R) is my goal.
>R is the bond distance I'm interested in; e.g. a C-O, C-Cl bond or , for testing purposes
>Na-Cl.
>
>But, unfortunately, wrong asymptotic behaviour (like a "size inconsistency problem") is
>observed in all cases: the "supermolecule's" solvation energy at large distances (10 or 20 A)
>is differing about more than 20 kcal/mole from the sum of the solvation energies of the two ions.
>
>My question is: is the problem known (references ?)? How can be it be accounted for ?
>Do I have to use specific energy terms given in gaussian's output and/or male a correction to them ?
>
>Any help is appreciated.
>
>Bye,
>
>Yours,
> Elmar
>
>
>
>
--
Jose A. Gascon - Postdoctoral Associate
Department of Chemistry - (203)432-5911; jose.gascon !! yale.edu
Yale University
P.O. Box 208107
New Haven, CT 06520-8107.
From chemistry-request@ccl.net Fri Jul 8 02:56:07 2005
Received: from poincare.ciril.fr (smtp.esstin.uhp-nancy.fr [194.214.217.19])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j686u1qF012356
for <chemistry !! ccl.net>; Fri, 8 Jul 2005 02:56:02 -0400
Received: from ptxavier (pt-xav.lctn.uhp-nancy.fr [193.50.239.125])
by poincare.ciril.fr (8.13.4/8.13.4/Guy-30-12-2004) with SMTP id j686tnqY003526
for <chemistry !! ccl.net>; Fri, 8 Jul 2005 08:55:50 +0200 (METDST)
From: "Xavier ASSFELD" <Xavier.Assfeld !! cbt.uhp-nancy.fr>
To: <chemistry !! ccl.net>
Subject: RE: dissociation problem in PCM model ?
Date: Fri, 8 Jul 2005 08:55:41 +0200
Message-ID: <NMEDKFNKILGNCLLLEKCPKEHBCDAA.Xavier.Assfeld !! cbt.uhp-nancy.fr>
MIME-Version: 1.0
Content-Type: text/plain;
charset="us-ascii"
Content-Transfer-Encoding: 7bit
X-Priority: 3 (Normal)
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0)
X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180
Importance: Normal
In-Reply-To: <20050707202935.GA10202 !! pc1.chemie.uni-kl.de>
X-Spam-Score: -2.599 () BAYES_00
X-Scanned-By: poincare.ciril.fr on 194.214.217.19
X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO
autolearn=failed version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Hey,
This is because of the cavity! At equilibrium distance, your system is in
one cavity, but at large distance two cavities are needed. Continuum models
are able to handle one cavity, not two. I'm not aware of program able to
take care of that.
Yours.
...Xav
Pr. Xavier Assfeld Xavier.Assfeld !! cbt.uhp-nancy.fr
Chimie et Biochimie theoriques T: (33) 3 83 68 43 82
Faculte des Sciences F: (33) 3 83 68 43 71
54506 Vandoeuvre, France http://www.cbt.uhp-nancy.fr
X> -----Message d'origine-----
X> De : Computational Chemistry List [mailto:chemistry-request !! ccl.net]De
X> la part de Elmar Gerwalin
X> Envoye : jeudi 7 juillet 2005 22:30
X> A : CHEMISTRY !! ccl.net
X> Objet : CCL: dissociation problem in PCM model ?
X>
X>
X> Hi,
X>
X> I'm trying to describe dissociation processes in some small
X> organic molecules.
X> Therefore, I'm using B3LYP+SCRF(C-PCM, solvent=methanol) single
X> point jobs to get the
X> solvation energy at each step. Finally, a potential energy curve
X> E(R) is my goal.
X> R is the bond distance I'm interested in; e.g. a C-O, C-Cl bond
X> or , for testing purposes
X> Na-Cl.
X>
X> But, unfortunately, wrong asymptotic behaviour (like a "size
X> inconsistency problem") is
X> observed in all cases: the "supermolecule's" solvation energy at
X> large distances (10 or 20 A)
X> is differing about more than 20 kcal/mole from the sum of the
X> solvation energies of the two ions.
X>
X> My question is: is the problem known (references ?)? How can be
X> it be accounted for ?
X> Do I have to use specific energy terms given in gaussian's
X> output and/or male a correction to them ?
X>
X> Any help is appreciated.
X>
X> Bye,
X>
X> Yours,
X> Elmar
X>
X>
X> --
X> ========================================================
X> Elmar Gerwalin , University of Kaiserslautern,Germany
X> Dept. of Theoretical Chemistry
X> elg !! chemie.uni-kl.de
X> ========================================================
X>
X>
X> -= This is automatically added to each message by the mailing script =-
X> To send e-mail to subscribers of CCL put the string CCL: on your
X> Subject: line
X> and send your message to: CHEMISTRY !! ccl.net
X>
X> Send your subscription/unsubscription requests to:
X> CHEMISTRY-REQUEST !! ccl.net
X> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
X>
X> If your is mail bouncing from ccl.net domain due to spam filters, please
X> use the Web based form from CCL Home Page
X> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
X>
X>
X>
X>
X>
From chemistry-request@ccl.net Fri Jul 8 11:16:43 2005
Received: from mrbusi2.netcologne.de (mrbusi2.netcologne.de [194.8.194.214])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68FGcQR002723
for <chemistry/at/ccl.net>; Fri, 8 Jul 2005 11:16:39 -0400
Received: from cosmologic.de (xdsl-213-196-241-161.netcologne.de [213.196.241.161])
by mrbusi2.netcologne.de (Postfix) with ESMTP
id 8CDF0240026; Fri, 8 Jul 2005 17:16:37 +0200 (CEST)
Message-ID: <42CE98D3.9040206/at/cosmologic.de>
Date: Fri, 08 Jul 2005 17:16:35 +0200
From: Andreas Klamt <klamt/at/cosmologic.de>
User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.6b) Gecko/20031205 Thunderbird/0.4
X-Accept-Language: en-us, en
MIME-Version: 1.0
To: chemistry/at/ccl.net
Cc: Elmar Gerwalin <elg/at/chemie.uni-kl.de>
Subject: Re: CCL: Fwd: dissociation problem in PCM model ?
References: <452bfca9f0024f1b3c7e931d0d8a8047/at/chem.umn.edu>
In-Reply-To: <452bfca9f0024f1b3c7e931d0d8a8047/at/chem.umn.edu>
Content-Type: text/plain; charset=us-ascii; format=flowed
Content-Transfer-Encoding: 7bit
X-Spam-Status: No, score=1.1 required=5.0 tests=FORGED_RCVD_HELO,
RCVD_IN_NJABL_PROXY autolearn=no version=3.0.4
X-Spam-Level: *
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Dear Elmar, dear Chris,
just as a note, COSMO at least in its newer implementations as in
TURBOMOLE should also give a rather reasonable and additive result for
the solvation energies in such cases. Nevertheless, you must take into
account that at low values of epsilon some of the electrostatic
interaction of the parts is left, especially if hey are ions. So it is
reasonable that you do not just get the sum of the energies of the
individually solvated parts, unless the distance is very large. But I
agree, that the problem you are reporting most likely does not result
> from this end.
Regards
Andreas
Christopher Cramer wrote:
> Elmar,
>
> My textbook, Essentials of Computational Chemistry, actually has a
> specific section (11.4.4 Potentials of Mean Force and Solvent
> Structure) that mentions your problem. The issue is that continuum
> models like the PCM variants involve the definition of a solute
> cavity, typically defined as roughly the union of a set of van der
> Waals spheres on all of the atoms. If you pull your solute apart,
> breaking a bond, at some point you will exceed van der Waals contact
> and the poor program has to decide what to do. It is quite unpleasant
> to solve the Poisson equation with two cavities in a dielectric
> continuum... If memory serves, PCM leaves some sort of neck between
> the two for awhile, so that there is still a single cavity, but this
> clearly soon becomes a bad approximation, since there is really
> solvent there. At some point, the program probably just delivers an
> error message (and a cryptic one, too, no doubt).
>
> But, if you compute the separated species individually, then there is
> no problem at all. Each has a well defined cavity and is infinitely
> far from anything but solvent. The two calculations will not agree,
> since the cavities were defined very differently.
>
> The only widely used continuum model that does NOT suffer from this
> discontinuity in a potential of mean force owing to cavity separation
> is the Generalized Born model, which takes atomic radii as inputs but
> does not use them to construct a formal cavity and is smooth and
> continuous over all distances.
>
> If you would like to try a GB model, you are welcome to employ one of
> our SMx solvation models, freely available in a variety of codes,
> including SMxGAUSS, which can either read a Gaussian output file as
> input and run as a stand-alone code, or can be driven by G03 using the
> "external" keyword. See comp.chem.umn.edu/mccdir/software.htm for full
> details.
>
> Best regards,
>
> Chris
>
> Begin forwarded message:
>
> *From: *Elmar Gerwalin <elg/at/chemie.uni-kl.de>
> *Date: *July 7, 2005 3:29:35 PM CDT
> *To: *CHEMISTRY/at/ccl.net
> *Subject: CCL: dissociation problem in PCM model ?
> Reply-To: *chemistry/at/ccl.net
>
> Hi,
>
> I'm trying to describe dissociation processes in some small
> organic molecules.
> Therefore, I'm using B3LYP+SCRF(C-PCM, solvent=methanol) single
> point jobs to get the
> solvation energy at each step. Finally, a potential energy curve
> E(R) is my goal.
> R is the bond distance I'm interested in; e.g. a C-O, C-Cl bond or
> , for testing purposes
> Na-Cl.
>
> But, unfortunately, wrong asymptotic behaviour (like a "size
> inconsistency problem") is
> observed in all cases: the "supermolecule's" solvation energy at
> large distances (10 or 20 A)
> is differing about more than 20 kcal/mole from the sum of the
> solvation energies of the two ions.
>
> My question is: is the problem known (references ?)? How can be it
> be accounted for ?
> Do I have to use specific energy terms given in gaussian's output
> and/or male a correction to them ?
>
> Any help is appreciated.
>
> Bye,
>
> Yours,
> Elmar
>
>
> --
> ========================================================
> Elmar Gerwalin , University of Kaiserslautern,Germany
> Dept. of Theoretical Chemistry
> elg/at/chemie.uni-kl.de
> ========================================================
>
>
>
> To send e-mail to subscribers of CCL put the string CCL: on your
> Subject: line
>
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST/at/ccl.net
>
>
> If your is mail bouncing from ccl.net domain due to spam filters,
> please
>
>
>
>
>
>
>
>
> --
>
> Christopher J. Cramer
> University of Minnesota
> Department of Chemistry
> 207 Pleasant St. SE
> Minneapolis, MN 55455-0431
> --------------------------
> Phone: (612) 624-0859 || FAX: (612) 626-2006
> Mobile: (612) 597-5275
> cramer/at/pollux.chem.umn.edu
> http://pollux.chem.umn.edu/~cramer
> (website includes information about the textbook "Essentials
> of Computational Chemistry: Theories and Models, 2nd Edition")
>
>
--
-----------------------------------------------------------------------------
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/at/cosmologic.de
web: www.cosmologic.de
-----------------------------------------------------------------------------
COSMOlogic
Your Competent Partner for
Computational Chemistry and Fluid Thermodynamics
-----------------------------------------------------------------------------
From chemistry-request@ccl.net Fri Jul 8 11:06:35 2005
Received: from smtp1.kodak.com (smtp1.kodak.com [192.232.121.200])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68F6WaX002258
for <chemistry/at/ccl.net>; Fri, 8 Jul 2005 11:06:33 -0400
Received: from roc-us-e1000-110.kodak.com (roc-us-e1000-110.kodak.com [192.232.121.190])
by smtp1.kodak.com (8.11.3/8.11.1) with SMTP id j68F6VL21345
for <chemistry/at/ccl.net>; Fri, 8 Jul 2005 11:06:31 -0400 (EDT)
Received: from (150.221.122.53) by roc-us-e1000-110.kodak.com via smtp
id 5c63_dddd707e_efc1_11d9_930a_0002b3eef597;
Fri, 08 Jul 2005 11:06:30 -0400
To: chemistry/at/ccl.net
Subject: Re: CCL: W:Solvation free energy for aromatic hydrocarbon
X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000
Message-ID: <OFE81A106F.0BF8804B-ON85257038.00519C7C/at/knotes.kodak.com>
From: david.giesen/at/kodak.com
Date: Fri, 8 Jul 2005 11:06:29 -0400
X-MIMETrack: Serialize by Router on KNOTES2/ISBP/EKC(652HF120|July 29, 2004) at 07/08/2005
11:06:31 AM,
Serialize complete at 07/08/2005 11:06:31 AM
MIME-Version: 1.0
Content-Type: text/plain; charset="us-ascii"
X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
I believe the confusion lies in the fact that a protein environment is not
well described by assuming it is the same as the gas phase. That phenyl
group in the protein is still "solvated" by the surrounding protein. The
important energetic measure in that case is not the (de)solvation energy
of the phenyl group in water, but the differential solvation energy of the
phenyl group between water and the protein environment.
Given a standard state of 1M concentration in the gas phase and solution
phase, and 298K, benzene has the following experimental solvation
energies: -0.9 kcal/mol in water, -4.0 kcal/mol in n-hexane, and -4.6
kcal/mol in benzene.
So you can see that transferring a benzene molecule from water to some
hydrocarbon-like environment is exothermic by ~3-4 kcal/mol, and for
similar reasons there is a negative (beneficial) energetic effect of
transfering the phenyl ring from water into the protein environment.
Dave Giesen
"Chemical, , Bond" <chemicalbond001/at/yahoo.com>
Sent by: "Computational Chemistry List" <chemistry-request/at/ccl.net>
07/07/2005 04:07 PM
Please respond to chemistry
To: chemistry/at/ccl.net
cc:
Subject: CCL: W:Solvation free energy for aromatic hydrocarbon
Hi there,
I am confused with a single concept: what should be the sign for the
solvation free energy for a fragment like phenyl?
There are many experimental data of solvation free energy for aromatic
hydrocarbons, such as benzene, naphthalene, etc, but they are all negative
surprisingly. I looked at several papers with models of solvation energy,
and their predictions all all have negative solvation energies for those
compounds, just like the experiments.
Typically when a phenyl group is transfered from water into protein, we
would like to say there is a negative(beneficial) desolvation energy, or
the usual called hydrophobic effect. And this has been used in tons of
models for protein simulation or protein-ligand binding. Note, in this
context, the solvation energy (from gas into water) is positive!
Is there something wrong over here? Or just some artifact from the
fitting?
Hope there would be some good comments.
Thanks a lot,
Bond
-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject:
line
and send your message to: CHEMISTRY/at/ccl.net
Send your subscription/unsubscription requests to:
CHEMISTRY-REQUEST/at/ccl.net
HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
If your is mail bouncing from ccl.net domain due to spam filters, please
use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
From chemistry-request@ccl.net Fri Jul 8 12:54:39 2005
Received: from mxsf31.cluster1.charter.net (mxsf31.cluster1.charter.net [209.225.28.130])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68GsbVp007720
for <chemistry$at$ccl.net>; Fri, 8 Jul 2005 12:54:37 -0400
Received: from mxip17a.cluster1.charter.net (mxip17a.cluster1.charter.net [209.225.28.147])
by mxsf31.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id j68GsaSa018617
for <chemistry$at$ccl.net>; Fri, 8 Jul 2005 12:54:36 -0400
Received: from unknown (HELO inspiron9100) (24.247.172.122)
by mxip17a.cluster1.charter.net with ESMTP; 08 Jul 2005 12:54:36 -0400
Message-Id: <44038i$15aakar$at$mxip17a.cluster1.charter.net>
X-IronPort-AV: i="3.93,274,1115006400";
d="scan'208"; a="1252348251:sNHT29271856"
From: "Jim Kress" <ccl_nospam$at$kressworks.com>
To: <chemistry$at$ccl.net>
Subject: RE: dissociation problem in PCM model ?
Date: Fri, 8 Jul 2005 12:54:06 -0400
MIME-Version: 1.0
Content-Type: text/plain;
charset="us-ascii"
Content-Transfer-Encoding: 7bit
X-Mailer: Microsoft Office Outlook, Build 11.0.6353
In-Reply-To: <42CDDC5D.30308$at$yale.edu>
thread-index: AcWD2Z58op0XFSQvRwaLmf8ZHKVxpQAAoXfg
X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
As I understand your problem, you are trying to determine the E vs R curve
for the dissociation of a bond. You have also found that the energy you get
at large R is inconsistent with what you expected with respect to the
expected dissociation products. For example, in NaCl you find it does not
dissociate to Na + Cl but instead it dissociates to Na+ + Cl-.
Assuming my understanding is correct, what you have encountered is a classic
problem with HF or DFT (single determinant) wave function application. This
is discussed in detail in the Computational Chemistry books by Jensen, by
Cramer, etc.
You need to use a different method to properly describe this dissociation.
Generalized Valence Bond (GVB) methods were developed by Goddard et al to do
this. They are implemented in PCGAMESS (and GAMESS) and are reasonably
straightforward to apply. You can also do a two configuration MCSCF or some
other size consistent approach that provides proper dissociation.
My preference in doing this for purposes like yours, is to use GVB. If you
want some help contact me off the list.
Jim
> -----Original Message-----
> From: Jose Gascon [mailto:jose.gascon$at$yale.edu]
> Sent: Thursday, July 07, 2005 9:52 PM
> To: chemistry$at$ccl.net
> Subject: CCL: dissociation problem in PCM model ?
>
>
> Elmar, as I understand, DFT cannot be used to calculate
> dissociation energies.
> Consider just the case of H2+ (the most trivial molecule).
> Here you will get the wrong assimptotic value. In fact
> Hartree-Fock will give you the exact answer.
> This is an intrinsic problem given by the fact that the
> density functionals are not known exactly. In the case of H2+
> this results in an electron that can literally interact with itself.
> My suggestion is to use MP2 or QCISD if you can afford it.
> Best, jose
>
> Elmar Gerwalin wrote:
>
> >Hi,
> >
> >I'm trying to describe dissociation processes in some small
> organic molecules.
> >Therefore, I'm using B3LYP+SCRF(C-PCM, solvent=methanol)
> single point
> >jobs to get the solvation energy at each step. Finally, a
> potential energy curve E(R) is my goal.
> >R is the bond distance I'm interested in; e.g. a C-O, C-Cl bond or ,
> >for testing purposes Na-Cl.
> >
> >But, unfortunately, wrong asymptotic behaviour (like a "size
> >inconsistency problem") is observed in all cases: the
> "supermolecule's"
> >solvation energy at large distances (10 or 20 A) is
> differing about more than 20 kcal/mole from the sum of the
> solvation energies of the two ions.
> >
> >My question is: is the problem known (references ?)? How can
> be it be accounted for ?
> >Do I have to use specific energy terms given in gaussian's
> output and/or male a correction to them ?
> >
> >Any help is appreciated.
> >
> >Bye,
> >
> >Yours,
> > Elmar
> >
> >
> >
> >
>
> --
> Jose A. Gascon - Postdoctoral Associate
> Department of Chemistry - (203)432-5911; jose.gascon$at$yale.edu
> Yale University P.O. Box 208107 New Haven, CT 06520-8107.
>
>
>
>
> -= This is automatically added to each message by the mailing
> script =-
> To send e-mail to subscribers of CCL put the string CCL: on
> your Subject: line
> and send your message to: CHEMISTRY$at$ccl.net
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST$at$ccl.net
> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
>
> If your is mail bouncing from ccl.net domain due to spam
> filters, please
> use the Web based form from CCL Home Page
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> -+-+-+-+-+
>
>
>
>
>
>
>
>
From chemistry-request@ccl.net Fri Jul 8 16:16:19 2005
Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68KGHI5019462
for <CHEMISTRY[at]ccl.net>; Fri, 8 Jul 2005 16:16:17 -0400
Received: from nobody by webmail.mta.ca with local (Exim 4.20)
id 1DqyLv-0005zb-Q4
for CHEMISTRY[at]ccl.net; Fri, 08 Jul 2005 16:17:35 -0300
Received: from 138.73.24.124 ( [138.73.24.124])
as user khunter[at]mailserv.mta.ca by webmail.mta.ca with HTTP;
Fri, 8 Jul 2005 16:17:35 -0300
Message-ID: <1120850255.42ced14fbf752[at]webmail.mta.ca>
Date: Fri, 8 Jul 2005 16:17:35 -0300
From: khunter[at]mta.ca
To: CHEMISTRY[at]ccl.net
Subject: CCL Macromodel conformation search
MIME-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit
X-Originating-IP: 138.73.24.124
X-Spam-Status: No, score=0.2 required=5.0 tests=FORGED_RCVD_HELO,NO_REAL_NAME
autolearn=no version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Was wondering if it was possible to do a conformational search with Macromodel
where one is changing the puckering in a five membered ring.
From chemistry-request@ccl.net Fri Jul 8 14:30:34 2005
Received: from mailTM.sued-chemie.de (mailtm.sued-chemie.de [195.145.99.198])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68IUWJQ012711
for <chemistry|at|ccl.net>; Fri, 8 Jul 2005 14:30:33 -0400
Received: by mailTM.sued-chemie.de (Postfix, from userid 65534)
id E7DA21A7714; Fri, 8 Jul 2005 20:33:32 +0200 (CEST)
Received: from mailtm2.sued-chemie.com (unknown [172.16.1.15])
by mailTM.sued-chemie.de (Postfix) with SMTP id 57F6D1A75B1
for <chemistry|at|ccl.net>; Fri, 8 Jul 2005 20:33:31 +0200 (CEST)
Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srv49003.scag.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713);
Fri, 8 Jul 2005 20:29:45 +0200
X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0
content-class: urn:content-classes:message
MIME-Version: 1.0
Content-Type: text/plain;
charset="iso-8859-1"
Subject: RE: W:Symmetry breaking during CASSCF
Date: Fri, 8 Jul 2005 14:29:43 -0400
Message-ID: <9DD56492790889439F731F5BD6DACA0009B63F8C|at|srvkyem1.americas.sc-world.com>
X-MS-Has-Attach:
X-MS-TNEF-Correlator:
Thread-Topic: W:Symmetry breaking during CASSCF
Thread-Index: AcWD2UP9NJ/abOpnQBy5Lv5RX7WRggAESgzQ
From: "Shobe, David" <dshobe|at|sud-chemieinc.com>
To: <chemistry|at|ccl.net>
X-OriginalArrivalTime: 08 Jul 2005 18:29:45.0384 (UTC) FILETIME=[03C6CA80:01C583EB]
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
X-Spam-Level:
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j68IUYJQ012715
Jahn-Teller effect, perhaps? Does the D2h geometry have degenerate orbitals which become non-degenerate once the symmetry is broken?
--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724
Don't bother flaming me: I'm behind a firewall.
-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request|at|ccl.net] On Behalf Of Gustavo, L.C., Moura
Sent: Friday, July 08, 2005 7:35 AM
To: chemistry|at|ccl.net
Subject: CCL: W:Symmetry breaking during CASSCF
Dear CCL Readers,
I have a planar conjugated organic molecule that, on paper, has D2h symmetry. I am working with the hypothesis that the molecule is a biradical singlet. I want to perform a CASSCF(2,2) on this molecule to estimate the biradical character of this molecule. When I calculate the molecule with the constraint that the molecule has D2h symmetry, the calculation has severe convergence problems. If I remove this constraint, the molecule distorts to a C2v symmetry and I obtain a biradical character ~20%. I checked the orbitals being used for the CASSCF calculation and they look right (one nonbonding and another slightly antibonding).
Is the situation described above correct? Can an organic molecule have such a symmetry breaking as a result of a CASSCF calculation? Is the molecule really a C2v system? Any suggestions are welcome.
Thank you very much in advance for your help.
Sincerely yours,
Gustavo L.C. Moura
gustavo|at|mercury.chem.pitt.edu
-= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY|at|ccl.net
Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net
HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
From chemistry-request@ccl.net Fri Jul 8 14:16:47 2005
Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5])
by server.ccl.net (8.13.1/8.13.1) with ESMTP id j68IGj6S012056
for <chemistry|at|ccl.net>; Fri, 8 Jul 2005 14:16:46 -0400
Received: from localhost (localhost.localdomain [127.0.0.1])
by localhost.sud-chemieinc.com (Postfix) with ESMTP id E07F73240F6
for <chemistry|at|ccl.net>; Fri, 8 Jul 2005 14:01:18 -0400 (EDT)
Received: from smtpgw.sud-chemieinc.com ([127.0.0.1])
by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024)
with ESMTP id 31226-07 for <chemistry|at|ccl.net>;
Fri, 8 Jul 2005 14:01:15 -0400 (EDT)
Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11])
by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 1A0563240D5
for <chemistry|at|ccl.net>; Fri, 8 Jul 2005 14:01:15 -0400 (EDT)
Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713);
Fri, 8 Jul 2005 14:15:07 -0400
X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0
content-class: urn:content-classes:message
MIME-Version: 1.0
Content-Type: text/plain;
charset="iso-8859-1"
Subject: RE: W:Solvation free energy for aromatic hydrocarbon
Date: Fri, 8 Jul 2005 14:15:06 -0400
Message-ID: <9DD56492790889439F731F5BD6DACA0007D78B38|at|srvkyem1.americas.sc-world.com>
X-MS-Has-Attach:
X-MS-TNEF-Correlator:
Thread-Topic: W:Solvation free energy for aromatic hydrocarbon
Thread-Index: AcWDRH/vV+tIfDDBSXqb7uHpd7wFzgAnOoLw
From: "Shobe, David" <dshobe|at|sud-chemieinc.com>
To: <chemistry|at|ccl.net>
X-OriginalArrivalTime: 08 Jul 2005 18:15:07.0157 (UTC) FILETIME=[F84FFC50:01C583E8]
X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed
version=3.0.4
X-Spam-Checker-Version: SpamAssassin 3.0.4 (2005-06-05) on server.ccl.net
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j68IGl6S012062
1. Although benzene and water are immiscible in the sense that if you put 50 mL H2O and 50 mL C6H6 in a vessel, close it, and shake vigorously, you will get two liquid phases, not one. However, there is an appreciable amount of water in the benzene phase, and an appreciable amount of benzene in the water phase. This experimental evidence suggests that the free energy change from vapor phase* to a dilute solution in water is negative, but the free energy change from the liquid benzene phase to a more concentrated aqueous solution is positive.
2. The movement of the phenyl group from solution to protein is not DEsolvation; instead solvation by water is replaced with more favorable solvation by the protein.
3. Phenyl groups (in this context) don't usually migrate by themselves; they are attached to some molecule. So the positive solvation energy of the phenyl group may actually represent the difference between the solvation energy of alanine v. phenylalanine, or of some other pair of molecules differing by a phenyl group.
--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724
Don't bother flaming me: I'm behind a firewall.
*The experiment uses liquid benzene but under ambient conditions the liqud-vapor equilibrium favors the liquid. If vapor to liquid is negative and liquid to dilute aq. soln. is negative, then vapor to dilute aq. soln. is negative also.
-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request|at|ccl.net] On Behalf Of Chemical, , Bond
Sent: Thursday, July 07, 2005 4:08 PM
To: chemistry|at|ccl.net
Subject: CCL: W:Solvation free energy for aromatic hydrocarbon
Hi there,
I am confused with a single concept: what should be the sign for the solvation free energy for a fragment like phenyl?
There are many experimental data of solvation free energy for aromatic hydrocarbons, such as benzene, naphthalene, etc, but they are all negative surprisingly. I looked at several papers with models of solvation energy, and their predictions all all have negative solvation energies for those compounds, just like the experiments.
Typically when a phenyl group is transfered from water into protein, we would like to say there is a negative(beneficial) desolvation energy, or the usual called hydrophobic effect. And this has been used in tons of models for protein simulation or protein-ligand binding. Note, in this context, the solvation energy (from gas into water) is positive!
Is there something wrong over here? Or just some artifact from the fitting?
Hope there would be some good comments.
Thanks a lot,
Bond
-= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY|at|ccl.net
Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net
HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+