From owner-chemistry@ccl.net Fri Oct 5 02:45:01 2007
From: "Alessandro Contini alessandro.contini,,unimi.it" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Quantitative measure for susceptibility to nucleophilic attack?
Message-Id: <-35320-071004132514-11411-UBH7XGzTCl+f5jSnjyxM3Q]|[server.ccl.net>
X-Original-From: Alessandro Contini <alessandro.contini _ unimi.it>
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Date: Thu, 04 Oct 2007 18:28:37 +0200
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Sent to CCL by: Alessandro Contini [alessandro.contini:+:unimi.it]
Hi,
you could eventually use the DFT-HSAB (Hard-Soft Acid-Base) methodology,
which was applied for the prediction of regioselectivity in
cycloaddition but it should be as well as adequate for your purposes.
See for example
A. Ponti and G. Molteni Chem. Eur. J. 2006, 12, 1156
Hope this helps
Alessandro
Il giorno gio, 04/10/2007 alle 13.31 +1000, Seth Olsen
s.olsen1/./uq.edu.au ha scritto:
> Sent to CCL by: Seth Olsen [s.olsen1],[uq.edu.au]
>
>
> Hi CCLers,
>
> I am interested in techniques which can provide a measure of
> susceptibility to nucleophilic attack in a particular fragment across a
> series of molecules. The goal is to have a quantitative measure of how
> different substitutents at another site affect the likelihood of
> nucleophilic attack at the site of interest.
>
> This is somewhat removed from the areas of electronic structure to which
> I am accustomed. I understand from reading Bader's book that divots and
> bumps in the lapacian of the density can be an indication of these, but
> I was wondering if there was something a little more straightforward to
> analyze.
>
> Can anyone point me to some references?
>
> Many Thanks,
>
> Seth
>
--
Dr. Alessandro Contini
Istituto di Chimica Organica "Alessandro Marchesini"
Universita' degli Studi di Milano, Facolta' di Farmacia
Via Venezian, 21 20133 Milano
Tel. +390250314480 Fax. +390250314476
e-mail alessandro.contini++unimi.it
skype alessandrocontini
From owner-chemistry@ccl.net Fri Oct 5 03:22:00 2007
From: "Lukasz Cwiklik cwiklik---gmail.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Output from Cubeman and probability density
Message-Id: <-35321-071004203356-13429-9ZtgIFAhCKB7QCadvm88KQ%x%server.ccl.net>
X-Original-From: "Lukasz Cwiklik" <cwiklik]_[gmail.com>
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Date: Fri, 5 Oct 2007 02:05:11 +0200
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Sent to CCL by: "Lukasz Cwiklik" [cwiklik_._gmail.com]
On 10/3/07, Soren Eustis soren%jhu.edu <owner-chemistry a ccl.net> wrote:
>
> Sent to CCL by: "Soren Eustis" [soren . jhu.edu]
> I am trying to calculate the probability density for a given diffuse singly occupied >molecular orbital. I have squared the orbital using cubeman, however I am not entirely >sure what the output is telling me. What I am interested in is creating a corresponding >contour plot where it encompasses 95% or 90%, etc. of the electron density. Thus >e/volume of orbital = 0.95, 0.9, etc. I ought to be able to take the probability density plot >as encompassing ~100% of the orbital volume (given that the cube was generated with a > massive number of steps).
>
> Any thoughts?
Hi Soren,
I think I can propose not very elegant but practical solution. You can
calculate a volume of electron density for your orbital's cube as a
function of isovalue in your cube file (collect volumes for increasing
isovalue). Then you can plot orbital contours for isovalues that
correspond to 0.95, 0.9 etc. of the total volume. You can use my
Python script cube_vol.py (from
http://cwiklik.wordpress.com/science/downloads/) that gives a volume
enclosed by isosurface for a given isovalue.
Best,
Lukasz
--
Lukasz Cwiklik
http://cwiklik.wordpress.com
From owner-chemistry@ccl.net Fri Oct 5 03:58:01 2007
From: "Dr. Ponnadurai Ramasami ramchemi[-]intnet.mu" <owner-chemistry(_)server.ccl.net>
To: CCL
Subject: CCL: Electron affinity
Message-Id: <-35322-071005035541-32167-O2AbIsL4llDsU18CaH+hRA(_)server.ccl.net>
X-Original-From: "Dr. Ponnadurai Ramasami" <ramchemi()intnet.mu>
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Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi[*]intnet.mu]
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Dear All
Electron affinity has been calculated using energy (neutral) - energy =
(anion)
However in some cases negative values are obtained.
Is this correct?
How to interpret? (I guess in term of stability of the two species)
Thanks for your comments
Ramasami
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<DIV><FONT face=3DArial size=3D2>Dear All</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Electron affinity has been calculated =
using energy=20
(neutral) - energy (anion)</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>However in some cases negative values =
are=20
obtained.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Is this correct?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>How to interpret? (I guess in term of =
stability of=20
the two species)</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Thanks for your comments</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></BODY></HTML>
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From owner-chemistry@ccl.net Fri Oct 5 05:58:02 2007
From: "Arvydas Tamulis tamulis(-)mserv.itpa.lt" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL:G: Why I obtained with G03 total energy differences for D- and L-serine
Message-Id: <-35323-071005050908-14663-XunOmlIblBAHoklGfeC3+g/a\server.ccl.net>
X-Original-From: Arvydas Tamulis <tamulis]_[mserv.itpa.lt>
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Date: Fri, 5 Oct 2007 12:08:26 +0300 (EEST)
MIME-Version: 1.0
Sent to CCL by: Arvydas Tamulis [tamulis(-)mserv.itpa.lt]
Dear Colleagues,
I have optimized geometry of D- and L-serine amino acid molecule by
using Gaussian03 DFT B3LYP and MP2 methods. It was surprise for me that
differences of total energies are equal approximately 2 kcal/mol.
B3LYP/cc-pVTZ gives lower total energy for the L-serine and
MP2/cc-pVTZ+IEFPCM gives lower total energy for D-serine.
For my opinion the non-relativistic methods must give the equal total
energy for D- and L-serine amino acid molecule.
Why I obtained with G03 these total energy differences?
With best regards,
Arvydas Tamulis
From owner-chemistry@ccl.net Fri Oct 5 06:57:00 2007
From: "Jens Spanget-Larsen spanget__ruc.dk" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL:G: Quantitative measure for susceptibility to nucleophilic attack?
Message-Id: <-35324-071005065605-2572-jHFFl46tukYrVxRyYwj10w!=!server.ccl.net>
X-Original-From: Jens Spanget-Larsen <spanget===ruc.dk>
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Date: Fri, 05 Oct 2007 12:55:54 +0200
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Sent to CCL by: Jens Spanget-Larsen [spanget[*]ruc.dk]
Dear Seth,
if you want something that is conceptually and calculationally very
simple, you may consider the semiempirical W-parameter
(J.Phys.Org.Chem.8, 496-505 (1995)). Another possibility is to compute
the electric potentials (EPs) provided by the keywords "density prop" in
Gaussian. The computed atomic EPs tend to be a measure of the
nucleophilic/electrophilic character of the different centers in the
molecule.
Yours, Jens >--<
------------------------------------------------------
JENS SPANGET-LARSEN Office: +45 4674 2710
Dept. of Science (18.1) Fax: +45 4674 3011
Roskilde University Mobile: +45 2320 6246
P.O.Box 260 E-Mail: spanget- -ruc.dk
DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget
------------------------------------------------------
Seth Olsen s.olsen1/./uq.edu.au wrote:
>
> Sent to CCL by: Seth Olsen [s.olsen1],[uq.edu.au]
>
>
> Hi CCLers,
>
> I am interested in techniques which can provide a measure of
> susceptibility to nucleophilic attack in a particular fragment across
> a series of molecules. The goal is to have a quantitative measure of
> how different substitutents at another site affect the likelihood of
> nucleophilic attack at the site of interest.
>
> This is somewhat removed from the areas of electronic structure to
> which I am accustomed. I understand from reading Bader's book that
> divots and bumps in the lapacian of the density can be an indication
> of these, but I was wondering if there was something a little more
> straightforward to analyze.
>
> Can anyone point me to some references?
>
> Many Thanks,
>
> Seth
>
From owner-chemistry@ccl.net Fri Oct 5 07:32:01 2007
From: "Jens Spanget-Larsen spanget[*]ruc.dk" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL: Electron affinity
Message-Id: <-35325-071005061342-15527-p6VSVvLT90GC6USJeuFTGg^-^server.ccl.net>
X-Original-From: Jens Spanget-Larsen <spanget:ruc.dk>
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Date: Fri, 05 Oct 2007 12:13:29 +0200
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Sent to CCL by: Jens Spanget-Larsen [spanget]|[ruc.dk]
Dear Ramasami,
negative electron affinity indicate that the anion in question is unstable
with respect to loss of an electron. Such temporary anions may be
detected by Electron Transmission Spectroscopy. See f.inst. the
bibliograp�hy by Paul Burrow: http://digitalcommons.unl.edu/physicsburrow/6/
Yours, Jens >--<
------------------------------------------------------
JENS SPANGET-LARSEN Office: +45 4674 2710
Dept. of Science (18.1) Fax: +45 4674 3011
Roskilde University Mobile: +45 2320 6246
P.O.Box 260 E-Mail: spanget#ruc.dk
DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget
------------------------------------------------------
Dr. Ponnadurai Ramasami ramchemi[-]intnet.mu wrote:
> Dear All
> Electron affinity has been calculated using energy (neutral) - energy
> (anion)
> However in some cases negative values are obtained.
> Is this correct?
> How to interpret? (I guess in term of stability of the two species)
> Thanks for your comments
>
> Ramasami
>
From owner-chemistry@ccl.net Fri Oct 5 08:08:00 2007
From: "Georg Lefkidis lefkidis^^^physik.uni-kl.de" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: AW: Electron affinity
Message-Id: <-35326-071005073650-23089-N+VUxF7tiQkQYi11YMx0+A _ server.ccl.net>
X-Original-From: "Georg Lefkidis" <lefkidis**physik.uni-kl.de>
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Date: Fri, 5 Oct 2007 13:05:12 +0200
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Sent to CCL by: "Georg Lefkidis" [lefkidis*o*physik.uni-kl.de]
Dies ist eine mehrteilige Nachricht im MIME-Format.
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Hi,
depending on the surroundings, it might be that an anion is more stable than
the neutral ion (e.g. in an ionic crystal). That depends on the specific
problem, some more detailed information is needed. Another aspect is to
ascertain that for both systems (neutral and anionic) you have indeed
obtained the electronic ground state. If for instance for the neutral system
HF converged to an excited state, then of course the electron affinity
result is plainly wrong.
Cheers
George
Dear All
Electron affinity has been calculated using energy (neutral) - energy
(anion)
However in some cases negative values are obtained.
Is this correct?
How to interpret? (I guess in term of stability of the two species)
Thanks for your comments
Ramasami
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<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi,<o:p></o:p></span></p>
<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>depending on the surroundings, it might be that an anion =
is more
stable than the neutral ion (e.g. in an ionic crystal). That depends on =
the
specific problem, some more detailed information is needed. Another =
aspect is
to ascertain that for both systems (neutral and anionic) you have indeed =
obtained
the electronic ground state. If for instance for the neutral system HF =
converged
to an excited state, then of course the electron affinity result is =
plainly
wrong.<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Cheers<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>George<o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
<p class=3DMsoNormal><span lang=3DEN-US =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Dear
All</span><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Electron
affinity has been calculated using energy (neutral) - energy =
(anion)</span><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>However
in some cases negative values are obtained.</span><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Is
this correct?</span><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>How
to interpret? (I guess in term of stability of the two =
species)</span><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Thanks
for your comments</span><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> <o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal><span =
style=3D'font-size:10.0pt;font-family:"Arial","sans-serif"'>Ramasami</spa=
n><o:p></o:p></p>
</div>
<div>
<p class=3DMsoNormal> <o:p></o:p></p>
</div>
</div>
</body>
</html>
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From owner-chemistry@ccl.net Fri Oct 5 09:54:00 2007
From: "Patrick Senet psenet-$-u-bourgogne.fr" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Quantitative measure for susceptibility to nucleophilic attack?
Message-Id: <-35327-071005084750-16022-UBYGUH3eSeYoR1xe8OMhUQ]~[server.ccl.net>
X-Original-From: Patrick Senet <psenet(_)u-bourgogne.fr>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Fri, 05 Oct 2007 14:04:55 +0200
MIME-Version: 1.0
Sent to CCL by: Patrick Senet [psenet{}u-bourgogne.fr]
Hi,
A recent application of Fukui functions and hardnesses to a distinguish
a series of molecules appear in the paper below where you will find also
key references of the literature on this topic.
P. Senet and F. Aparicio, "Density functional theory fragment
descriptors to quantify the reactivity of a molecular family:
Application to amino acids",
J. Chem. Phys. 126, 145105 (2007).
Best regards,
Patrick
Seth Olsen s.olsen1/./uq.edu.au a �crit :
>
> Sent to CCL by: Seth Olsen [s.olsen1],[uq.edu.au]
>
>
> Hi CCLers,
>
> I am interested in techniques which can provide a measure of
> susceptibility to nucleophilic attack in a particular fragment across
> a series of molecules. The goal is to have a quantitative measure of
> how different substitutents at another site affect the likelihood of
> nucleophilic attack at the site of interest.
>
> This is somewhat removed from the areas of electronic structure to
> which I am accustomed. I understand from reading Bader's book that
> divots and bumps in the lapacian of the density can be an indication
> of these, but I was wondering if there was something a little more
> straightforward to analyze.
>
> Can anyone point me to some references?
>
> Many Thanks,
>
> Seth
>
From owner-chemistry@ccl.net Fri Oct 5 11:08:00 2007
From: "Jozsef Csontos jozsefcsontos*|*creighton.edu" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL:G: Why I obtained with G03 total energy differences for D- and L-serine
Message-Id: <-35328-071005110436-28199-eFlu6LBm7LPdrndBuUhQ5w#%#server.ccl.net>
X-Original-From: Jozsef Csontos <jozsefcsontos ~~ creighton.edu>
Content-Transfer-Encoding: 7bit
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Date: Fri, 05 Oct 2007 10:04:24 -0500
Mime-Version: 1.0
Sent to CCL by: Jozsef Csontos [jozsefcsontos%a%creighton.edu]
Hi,
because you optimized both stereoisomers (at least it seems to me from
your letter) you should check whether the obtained geometries are still
mirror images. I guess they are not.
Try to optimize one of the stereoismers (then a frequency analysis to
make sure the obtained geometry is a minimum) then just multiply every
z-coordinate by -1.0 and you obtained the other isomer as well. Finally
a frequency analysis will tell you everything. This way you shouldn't
get substantial energy difference, on the same level, between the
isomers.
Hope it helps,
Jozsef
On Fri, 2007-10-05 at 12:08 +0300, Arvydas Tamulis
tamulis(-)mserv.itpa.lt wrote:
> Sent to CCL by: Arvydas Tamulis [tamulis(-)mserv.itpa.lt]
> Dear Colleagues,
>
> I have optimized geometry of D- and L-serine amino acid molecule by
> using Gaussian03 DFT B3LYP and MP2 methods. It was surprise for me that
> differences of total energies are equal approximately 2 kcal/mol.
> B3LYP/cc-pVTZ gives lower total energy for the L-serine and
> MP2/cc-pVTZ+IEFPCM gives lower total energy for D-serine.
> For my opinion the non-relativistic methods must give the equal total
> energy for D- and L-serine amino acid molecule.
> Why I obtained with G03 these total energy differences?
>
> With best regards,
> Arvydas Tamulis>
>
>
--
Jozsef Csontos, Ph.D.
(jozsefcsontos_at_creighton.edu)
Department of Biomedical Sciences
Creighton University,
Omaha, NE
From owner-chemistry@ccl.net Fri Oct 5 11:43:00 2007
From: "Mireille Viviane Krier mv.krier*googlemail.com" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: InChI parameters in pubchem
Message-Id: <-35329-071005040353-5776-Zbt/rYkIoXpbperNZJy7bQ%server.ccl.net>
X-Original-From: "Mireille Viviane Krier" <mv.krier%a%googlemail.com>
Date: Fri, 5 Oct 2007 04:03:49 -0400
Sent to CCL by: "Mireille Viviane Krier" [mv.krier ~~ googlemail.com]
Dear CCLers,
I want to share with you a recent e-mail exchange I had with Evan Bolt (NIH/NLM/NCBI). It answers to the question : where do I get the information about the parameters used to calculate the InChI for a compound in PubChem?
Here Evan's kind answer:
The InChI version and parameters are detailed in the ASN.1 and XML data for each compound. For example, for aspirin, you can find the information you are seeking by viewing the ASN.1 record:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2244&disopt=DisplayASN1
If you scroll down to the InChI property record, you will find:
{
urn {
label "InChI",
datatype string,
parameters "options {auxnonr donotaddh w0 fixedh recmet newps}",
implementation "E_INCHI",
version "1.0.1",
software "InChI",
source "nist.gov",
release "2007.09.04"
},
value sval "InChI=1/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H
,11,12)/f/h11H"
},
The InChI version is (currently) 1.0.1. We are using the parameter options "auxnonr donotaddh w0 fixedh recmet newps". We are (currently) using the InChI implementation within Cactvs. How we calculate our properties is subject to change, so we detail this information directly within the archive record.
I hope it can be useful for you.
Enjoy,
Mireille
From owner-chemistry@ccl.net Fri Oct 5 12:18:00 2007
From: "Jamie Rintelman rintjm() yahoo.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Gaussian parallelism and parallelism in general
Message-Id: <-35330-071005060237-32169-bTXbk1GmsQF8sskol5MgtA]_[server.ccl.net>
X-Original-From: Jamie Rintelman <rintjm- -yahoo.com>
Content-Transfer-Encoding: 7bit
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Date: Fri, 5 Oct 2007 10:02:23 +0100
Mime-Version: 1.0 (Apple Message framework v752.2)
Sent to CCL by: Jamie Rintelman [rintjm-$-yahoo.com]
Jeff,
I'm jumping in a bit late here, but I think that you're forgetting
GAMESS (maintained at ISU, and free). The MP2 energy and gradient,
MCSCF energy and hessians, among other things all scale very well up
to 100s or even 1000+ processors. These all use the Distributed Data
Interface of Graham Fletcher, Mike Schmidt, Ryan Olson et al.
Regards,
Jamie
On Oct 1, 2007, at 11:07 PM, Jeff Hammond jeff.science * gmail.com
wrote:
>
> Getting scalability beyond dozens of processors for quantum chemical
> codes is very difficult and has, to my knowledge, only been achieve by
> two kinds of developers: those using Global Arrays (NWChem, MolPro,
> UTChem) and those named Curt Janssen (MPQC). Please correct me if I
> have omitted anyone deserving.
>
> Jeff
>
From owner-chemistry@ccl.net Fri Oct 5 12:53:00 2007
From: "Negar Rajabi krajabi+*+mun.ca" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL:G: Inaccurate quadrature in caldsu
Message-Id: <-35331-071005104753-24724-9ZtgIFAhCKB7QCadvm88KQ{:}server.ccl.net>
X-Original-From: Negar Rajabi <krajabi*_*mun.ca>
Content-Transfer-Encoding: 8bit
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Date: Fri, 5 Oct 2007 11:24:18 -0230
MIME-Version: 1.0
Sent to CCL by: Negar Rajabi [krajabi..mun.ca]
Hi,
I am trying to optimize adenine K-bound dimer at B3LYP/6-31+g(d,p)using G03 but
I've got the error (Inaccurate quadrature in caldsu ) each time. I tried
different guess functions such as INDO & Huckle but the error still exsits. I
read the previous messages regarding to this error:
{Sent to CCL by: Kadir Diri [kadir(a)visual1.chem.pitt.edu]
Hi! I thought this was a problem with the default initial guess, but if other
methods like indo fail too, you probabbly have a really bad guess. Since you
are using ghost atoms, I tend to think that you maybe running into severe
linear dependency problems. If that is the case, you should spend some time
improving your basis set.
kadir
CCL wrote:
Sent to CCL by: Oluwakemi.Oloba|a|mail.uh.edu
Hello
Pls can anyone help me with this i am runiung a a calculation on g03 with the
Bq
atoms but it keeps coming out with the error "inaccurate quadrature in caldsu"
i have tried using guess=indo but it still does not work
Thanks a lot
Kemi Oloba>}
but it's not the case. I would appreciate any suggections!
Negar
From owner-chemistry@ccl.net Fri Oct 5 13:29:01 2007
From: "Anouar Benali Anouar.Benali-#-ensiacet.fr" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Question: Best combination of Linux OS & compiler for Gaussian03
Message-Id: <-35332-071005085721-22824-ZWRW2t5blh62dMU1PTqiKw++server.ccl.net>
X-Original-From: Anouar Benali <Anouar.Benali.:.ensiacet.fr>
Content-Transfer-Encoding: 8bit
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Date: Fri, 05 Oct 2007 14:29:41 +0200
MIME-Version: 1.0
Sent to CCL by: Anouar Benali [Anouar.Benali^-^ensiacet.fr]
Yangsoo Kim vsmember-x-gmail.com a �crit :
>Sent to CCL by: Yangsoo Kim [vsmember]![gmail.com]
>Dear all,
>
>It looks like the recommendation from Gaussian company is not fresh enough
>for the Linux OS & compiler selection when a newer hardware system is used.
>According to their website (http://www.gaussian.com/g03_plat.htm), SuSE
>Linux 9.0, 9.1, 9.2, 9.3; SuSE Linux Enter. Server 9 SP3; RedHat Enterprise
>Linux 4 Update 2 should be used with the compiler version of Portland F77
>6.1-1, while newer computer hardware (CPU, M/B...) is coming nearly every 6
>month.
>
>It is, of course, understandable that Gaussian cannot update their test for
>all the new computer specs. On the other hand, however, it is critical for
>the end user to set up the fast and reliable system for running Gaussian.
>
>For example, INTEL Core2Quad Q6600 on [GIGABYTE]GA-G33-DS3R system with
>SATA2 HD that recently we purchased refused to install the old version of
>SuSe that Gaussian recommend due to the lack of drivers.
>
>My focus is how we could choose the most efficient (fast + stable) Linux OS
>+ compiler for the newer hardware? More specifically, what OS & compiler
>version should be used for the INTEL Core2Quad Q6600 on
>[GIGABYTE]GA-G33-DS3R system? Should we use Portland F77 instead of Intel
>compiler all the time, even if it is known that Intel hardware performance
>enhances a lot when Intel compiler is used?
>
>I believe Gaussian cannot test all the possible combinations of
>hardware/OS/compiler, so it might be useful to setup a user report system
>with a bench test problem on various different combination of
>hardware/OS/compiler, if not already exist.
>
>Any comment is greatly appreciated, and I'll summarize the answers on
>request.
>
>Yangsoo Kim, Ph.D.>
>
>
>
>
Hi
I had a problem with gaussian installation with fedora... according to
gaussian developpers, it wouldn't work with other linux distribs except
the ones titled on their web site... but after wandering in half a
milion forums, i found a way to make it work with all Fedora
distributions... (didn't test with the rest...)
the main problem comes from the writing on some wrong sector on the hard
disk... so the only thing to do is adding to the file* /etc/rc.local*
the following line... and everything will work...
*echo 0 > /proc/sys/kernel/randomize_va_space*
if you need more just contact me... i have written a little helper in
addition to the binaries installation files provided by gaussian
Anouar Benali
Ph.D, Student
From owner-chemistry@ccl.net Fri Oct 5 14:02:00 2007
From: "Alexandre Hocquet alexandre.hocquet*_*ensic.inpl-nancy.fr" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL: Quantitative measure for susceptibility to nucleophilic attack?
Message-Id: <-35333-071005121815-15877-rNabDCjNpjqL7SYZZ8JKWQ]^[server.ccl.net>
X-Original-From: Alexandre Hocquet <alexandre.hocquet|a|ensic.inpl-nancy.fr>
Content-Transfer-Encoding: 8bit
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Date: Fri, 05 Oct 2007 17:47:27 +0200
MIME-Version: 1.0
Sent to CCL by: Alexandre Hocquet [alexandre.hocquet+*+ensic.inpl-nancy.fr]
>> I am interested in techniques which can provide a measure of
>> susceptibility to nucleophilic attack in a particular fragment across
>> a series of molecules. The goal is to have a quantitative measure of
>> how different substitutents at another site affect the likelihood of
>> nucleophilic attack at the site of interest.
>>
>> This is somewhat removed from the areas of electronic structure to
>> which I am accustomed. I understand from reading Bader's book that
>> divots and bumps in the lapacian of the density can be an indication
>> of these, but I was wondering if there was something a little more
>> straightforward to analyze.
>>
>> Can anyone point me to some references?
In addition to the the work of Senet, you may want to have a look at
this paper :
Conceptual Density Functional Theory
P. Geerlings,* F. De Proft, and W. Langenaeker
Chem. Rev., 103 (5), 1793 -1874, 2003
It presents the framework of conceptual dft, a paradigm where you can
surely find tools to calculate what you need.
One of these tools, the dual descriptor, can map quantitatively the
nucleophilic and electrophilic regions within a molecule. it has been
presented in this paper :
Morell, C.; Grand, A.; Toro-Labb�, A. J. Phys.Chem. A 2005, 109,205
--
***********************************************
Alexandre Hocquet
Ecole Europ�enne d'Ing�nieurs en G�nie des Mat�riaux
6, rue Bastien Lepage 54010 Nancy Cedex
Alexandre.Hocquet[-]eeigm.inpl-nancy.fr
http://www.eeigm.inpl-nancy.fr/~hocque23/
***********************************************
From owner-chemistry@ccl.net Fri Oct 5 15:31:00 2007
From: "William F. Coleman wcoleman+/-wellesley.edu" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: Why I obtained with G03 total energy differences for D- and L-serine
Message-Id: <-35334-071005152829-13629-dCTgd9thkhghu+s8cjmZ7g() server.ccl.net>
X-Original-From: "William F. Coleman" <wcoleman-$-wellesley.edu>
Content-Transfer-Encoding: 8bit
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Date: Fri, 05 Oct 2007 14:53:04 -0400
MIME-Version: 1.0
Sent to CCL by: "William F. Coleman" [wcoleman===wellesley.edu]
One way to invert stereochemistry is with the free DSV Visualizer
(http://www.accelrys.com/products/downloads/ds_visualizer/index.html).
GaussView 4 will also do this, they say, but I haven't received ours yet.
I would take one isomer, minimize it using the desired model chemistry,
and then invert it and calculate the energy of the other isomer. Even
with something as simple as serine there will be many local minima arising
> from rotations about the OH, NH2 and carboxyl groups that producing an
exact mirror image by optimization of two independently drawn structures
will be a low probability event.
Cheers,
Flick
_______________
William F. Coleman
Professor of Chemistry
Wellesley College
Wellesley MA 02481
on leave 2007-08 - please contact via email only
wcoleman:wellesley.edu
www.wellesley.edu/Chemistry/colemanw.html
Editor, JCE WebWare and JCE Featured Molecules
http://www.jce.divched.org/JCEDLib/WebWare/
http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html
From owner-chemistry@ccl.net Fri Oct 5 21:19:01 2007
From: "Sengen Sun sengensun]-[yahoo.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: Quantitative measure for susceptibility to nucleophilic attack?
Message-Id: <-35335-071005205018-16712-ni9WRYepUmChYWfkLaqFHw:server.ccl.net>
X-Original-From: Sengen Sun <sengensun_-_yahoo.com>
Content-Transfer-Encoding: 8bit
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Date: Fri, 5 Oct 2007 16:50:08 -0700 (PDT)
MIME-Version: 1.0
Sent to CCL by: Sengen Sun [sengensun[*]yahoo.com]
I would say that none of those published approaches
has a generality in measuring nucleophilicity or
electrophilicity. They are rough approximations and
useful in differently limited degrees. Chemists have a
general philosophical difficculty here: what are
organic chemical rreactions? and how do they take
place? We need to clearly define these challenges in
order to make significant progress in prediction of
organic chemical reactions. There have been many
oversimplied and/or wrong statements on chemical
reactions in the literature. Here I'd like to post a
comment I wrote 6 months ago to criticize such a wrong
statement. To me, this is a very important discussion
about the philosophical challenge in prediction of
chemical reactions. I welcome any comments. Thanks.
>
------------------------------------
.
In the paper by Balanarayan et al. (JPC A 2007, 111,
2733-2738), the authors attempt to address the
electronic mechanism of concerted cycloadditions based
on molecular electrostatic potential topography
(MESP). Based on MESP data along the IRC, they apply a
key statement "electron flow is always toward the
positive potential". I agree that the their final
conclusions on the mechanisms of these two particular
reactions are coincidentally correct. But this key
statement above is false in many organic chemical
reactions.
.
The authors emphasized that MESP is a parameter
superior to any other kind of parameters that all
failed. But we must recognize that MESP is nothing but
a special way of formulating electron distribution in
the force field of nuclei. MESP is not more than a
state property corresponding to an equilibrated
stationary state. Typical examples that MESP cannot
address include two Diels-Alder reactions of
1,3-butadiene with ethene and maleic anhydride. The
slides of my presentation on the dynamic issues on the
parent Diels-Alder reaction are in the ccl.net web
site:
http://www.ccl.net/cca/documents/ConcertedCycloadditons_2/
A collision between ethene and 1,3-butadiene creates
two spots of more positive electrostatic potential at
the two sigma-bond forming locations, a consequence of
the force field overlapping of the carbon nuclei at
the two pairs of reaction centers. Four of the six pi
electrons are relocated to occupy these two spots to
form two new sigma bonds. We cannot develop a
mathematical parameter (like MESP) to indicate the
electron migration, based on our current knowledge of
quantum mechanics. What we can think is the electron
flow in one cyclic direction as indicated by three
full arrows as the electronic mechanism. Such a
mechanism is documented in some textbooks (Fox, M. A;
Whitesell, J. K. Organic Chemistry, 2nd Ed. Jones &
Bartlett Publishers, Sudbury, Massachusetts, 1997,
p288). All the computational data published in the
literature are artificial effects and do not mean
anything about the electronic dynamics or mechanism.
.
In the parent Diels-Alder reaction, a collision
induces positive electrostatic potential for electrons
to move in to form the two new sigma bonds. But we
cannot develop a mathematical parameter to indicate
the more positive potential, simply because electrons
occupy these spots as soon as they are created in a
collision. This is what the word "dynamics" and
chemical reaction are all about. This is the essence
of the collision-induced electron reorganization,
which distinguishes from any other causes of chemical
reactions such as MESP and orbitals:
http://ccl.net/cca/documents/ConcertedCycloadditons/
.
That "electron flow is always toward the positive
potential" is always true in this "dynamic" sense for
closed-shell reactions. It is because electrons
immediately occupy a spot of more positive
electrostatic potential as soon as the positive
electrostatic potential is created by a collision, an
equilibrated stationary state along the IRC of a
concerted reaction does not contain any appropriate
information of the electronic dynamics on a rigorous
theoretical basis, no matter what parameters are used.
.
While the collision-induced electron reorganization
has a general meaning, a chemical bond-forming process
always takes advantage of the existing MESP of
reactants. The charge neutralization based on MESP
drives essentially all linear bond-forming processes
in closed shell reactions. But concerted cycloadditons
are a class of special, very stimulating, and
obfuscating chemical reactions, and their electronic
mechanisms have remained unsolved for nearly 80 years.
Even the simplest reaction between ethylene and
fulminic acid has been so controversial and attracted
several research groups in the world.
.
I think that there are two critical issues with the
concerted reactions. First, as the two new sigma bonds
are formed concurrently, a conflict arises when they
cannot take the advantage of charge neutralization in
the same time. There are a vast number of reactions in
which only one of them can take the advantage of
charge neutralization, while there is a forced process
in the other bond-forming location where the electrons
have to move towards the more negative or less
positive MESP, contradictory to the key statement used
by Balanarayan et al.. In these cases, electrons still
always move "dynamically" towards the positive
electrostatic potential at the two sigma-bond-forming
locations. The dynamic force behind the scene can
drive the changes of state properties such as MESP.
This dynamic event and related mechanism cannot be
correctly resolved by the MESP data along the IRC.
.
Secondly, the regioselectivity in concerted
cycloadditions is probably the most interesting
chemical phenomena and has not been described
theoretically. The typical examples include acrolein
dimerization and the reaction between fulminic acid
and methyl acrylate. The regioselectivity is against
our simple intuition of charge neutralization based on
state properties of equilibrated stationary state
including MESP. Chemists have ever ignored the
physical and dynamic electronic reorganization, and
wrongly attributed the regioselectivity to the orbital
interactions that do not have an understandable
physical meaning but are just mathematical operations.
Balanarayan et al. also use the word "subjectivity"
for orbitals and related parameters in their paper,
which I agree absolutely. Then, the challenge and
controversies of the regioselectivity in concerted
cycloadditions remain outstanding for theoretical
chemists.
.
In the chemical literature, we have many scattered
rules for different reactions. An "understanding" of a
single reaction often is meaningless for another even
very closely-related one. If theoretical chemistry
were about to use a different rule for description of
a different reaction, it would be ridiculous science.
I would conclude that MESP along the IRC has a severe
limitation to understand the electronic dynamics in
concerted cycloadditions. I don�t believe that they
have an "attractive method" until they show me how to
use their methods to describe (or to think) these four
reactions: the reaction between fulminic acid and
methyl acrylate, acrolein dimerization, the parent
Diels-Alder reaction, and the reaction between maleic
anhydride and 1,3-butadiene.
____________________________________________________________________________________
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