From owner-chemistry@ccl.net Wed Jul  8 10:13:00 2009
From: "Schwobel, Johannes J.Schwobel%x%ljmu.ac.uk" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: 1. Steric hindrance 2. TS (Michael Addition)
Message-Id: <-39709-090708083439-1902-/MWbWL/AsRsw0laBZtNizA[a]server.ccl.net>
X-Original-From: "Schwobel, Johannes" <J.Schwobel]_[ljmu.ac.uk>
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Date: Wed, 8 Jul 2009 12:17:02 +0100
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Sent to CCL by: "Schwobel, Johannes" [J.Schwobel/./ljmu.ac.uk]
Dear CCLers,
=20
I would appreciate your advice on two questions:
=20
I'm calculating reactivity and transition states (TS) for the Michael =
addition reaction (soft nucleophiles with alpha,beta unsaturated =
compounds) at B3LYP level. Obviously, it seems to be very difficult to =
locate a TS. Does anyone have any experience with theoretical TS =
calculations of this type of reaction or know any further papers about =
that?
=20
If there is a substituent in alpha-position, reactivity decreases =
significantly. This might have electronic or steric effects. For the =
latter I want to know: Is there any descriptor or parameter available to =
quantify the local (e.g. atom-centered) steric hindrance?
=20
Thanks a lot in advance!
Johannes Schwobel
=20


From owner-chemistry@ccl.net Wed Jul  8 11:24:00 2009
From: "andras.borosy!=!givaudan.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: mathematical methods in the study of chemical questions :-)
Message-Id: <-39710-090708111207-26198-1mjtrxUX6x2X9OnP/TlhRA**server.ccl.net>
X-Original-From: andras.borosy_._givaudan.com
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Date: Wed, 8 Jul 2009 16:35:42 +0200
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Sent to CCL by: andras.borosy(0)givaudan.com
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Every attempt to employ mathematical methods in 
the study of chemical questions must be considered
profoundly irrational and contrary to the spirit 
of chemistry.... if mathematical analysis should 
ever hold a prominent place in chemistry -- an 
aberration which is happily almost impossible -- 
it would occasion a rapid and widespread 
degeneration of that science.    

- Auguste Comte 

http://home.att.net/~quotations/science.html 
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<br><tt><font size=3>Every attempt to employ mathematical methods in &nbsp;
<br>
the study of chemical questions must be considered<br>
profoundly irrational and contrary to the spirit &nbsp;<br>
of chemistry.... if mathematical analysis should &nbsp;<br>
ever hold a prominent place in chemistry -- an &nbsp; &nbsp;<br>
aberration which is happily almost impossible -- &nbsp;<br>
it would occasion a rapid and widespread &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<br>
degeneration of that science. &nbsp; &nbsp;</font></tt><font size=3><br>
</font><tt><font size=3><br>
- Auguste Comte</font></tt><font size=3> <br>
</font><font size=2 color=blue><u><br>
</u></font><a href=http://home.att.net/~quotations/science.html><font size=2 color=blue><u>http://home.att.net/~quotations/science.html</u></font></a><font size=3>
</font>
--=_alternative 00502C99C12575ED_=--


From owner-chemistry@ccl.net Wed Jul  8 11:59:01 2009
From: "Jan Labanowski janl . speakeasy.net" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: CCL will run unattended for two weeks
Message-Id: <-39711-090708114113-3913-t0SN11IkKZB+vxLvWcdWfg-#-server.ccl.net>
X-Original-From: Jan Labanowski <janl*_*speakeasy.net>
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Date: Wed, 08 Jul 2009 11:41:00 EDT
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Sent to CCL by: Jan Labanowski [janl() speakeasy.net]
Dear CCL,

I will take two week vacations starting Sat Jul 11. Of course, I am taking =
my
laptop with me, but the servers will be unattended during these two weeks --
there will be nobody around "to push the button". So keep your fingers cros=
sed
that we do not have some power outages or a heat wave in Ohio.

Best,
The CCL maintainer,

Jan Labanowski
jkl-,-ccl.net


From owner-chemistry@ccl.net Wed Jul  8 12:33:01 2009
From: "Grigoriy Zhurko reg_zhurko,,chemcraftprog.com" <owner-chemistry()server.ccl.net>
To: CCL
Subject: CCL:G: How the Z-matrix is implemented
Message-Id: <-39712-090708120323-18665-GdSaKIKxV14bemziIfyCTA()server.ccl.net>
X-Original-From: Grigoriy Zhurko <reg_zhurko===chemcraftprog.com>
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Date: Wed, 8 Jul 2009 18:48:12 -0700
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Sent to CCL by: Grigoriy Zhurko [reg_zhurko::chemcraftprog.com]
  Hello,

  Can anyone suggest a paper where the implementation of standard Z-matrix (used in Gaussian, Gamess, etc) is described? I mean the formulas for calculating the Cartesian coordinates of atoms by their internal coordinates (distances, angles and dihedrals).

  Thanks in advance,
  Grigoriy Zhurko.


From owner-chemistry@ccl.net Wed Jul  8 13:13:00 2009
From: "Pavle Mocilac pavle.mocilac2]|[mail.dcu.ie" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: CBS-Q method in druglike molecules
Message-Id: <-39713-090708124854-8468-MSquwZAphOneGZ3KEO+lqA++server.ccl.net>
X-Original-From: "Pavle  Mocilac" <pavle.mocilac2(-)mail.dcu.ie>
Date: Wed, 8 Jul 2009 12:48:50 -0400


Sent to CCL by: "Pavle  Mocilac" [pavle.mocilac2{:}mail.dcu.ie]
My dear colleagues,

Recently I sent the question about the calculation of pKa of small druglike molecules. The method asks employing high accuracy models like G1, G2, CBS-Q in order to get accurate Free Gibbs energies using Gaussian 09, of course.. 
Now, it seems to me that this model works OK, and fast enough for very small molecules up to 10 or 12 atoms (hydrogen included). But, my molecule has 25 atoms and currently is stacked at QCISD(T)/6-31+G(d') step, calculating something called "triples" for more than 2 days!!!!!
I would like to emphasize that this job is being calculating with Gaussian 09 (Linux version), using lots of memory () and 8 processors at SGI Altix ICE 8200EX. 
What is the limit of CBS-Q method regarding the number of atoms? Is 25 atoms too much? Is there any option to use some kind of additional keywords to exclude "triples" calculation at QCISD(T)/6-31+G(d') step? Will that exclusion hamper accurate result? Is it better to use CBS-4M?


From owner-chemistry@ccl.net Wed Jul  8 14:01:01 2009
From: "Jonas Baltrusaitis jasius_1__yahoo.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL:G: How the Z-matrix is implemented
Message-Id: <-39714-090708134356-17163-GyuDu+/fWHKSE7wpl7drag(0)server.ccl.net>
X-Original-From: Jonas Baltrusaitis <jasius_1+/-yahoo.com>
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Date: Wed, 8 Jul 2009 09:43:40 -0700 (PDT)
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Sent to CCL by: Jonas Baltrusaitis [jasius_1^yahoo.com]

Grigoryi,=0A=0Ayou might want to contact OpenBabel or Avogadro developers a=
s they have this conversion implemented=0A=0AJonas=0A=0A--- On Wed, 7/8/09,=
 Grigoriy Zhurko reg_zhurko,,chemcraftprog.com <owner-chemistry^^^ccl.net> wr=
ote:=0A=0A> From: Grigoriy Zhurko reg_zhurko,,chemcraftprog.com <owner-chem=
istry^^^ccl.net>=0A> Subject: CCL:G: How the Z-matrix is implemented=0A> To: =
"Baltrusaitis, Jonas " <jasius_1^^^yahoo.com>=0A> Date: Wednesday, Ju=
ly 8, 2009, 6:48 PM=0A> =0A> Sent to CCL by: Grigoriy Zhurko=0A> [reg_zhurk=
o::chemcraftprog.com]=0A> =A0 Hello,=0A> =0A> =A0 Can anyone suggest a pape=
r where the implementation=0A> of standard Z-matrix (used in Gaussian, Game=
ss, etc) is=0A> described? I mean the formulas for calculating the Cartesia=
n=0A> coordinates of atoms by their internal coordinates=0A> (distances, an=
gles and dihedrals).=0A> =0A> =A0 Thanks in advance,=0A> =A0 Grigoriy Zhurk=
o.=0A> =0A> =0A> =0A> -=3D This is automatically added to each message by t=
he=0A> mailing script =3D-=0A> To recover the email address of the author o=
f the message,=0A> please change=0A> the strange characters on the top line=
 to the ^^^ sign. You=0A> can also=0A> look up the X-Original-From: line in t=
he mail header.=0A> =0A> E-mail to subscribers: CHEMISTRY^^^ccl.net=0A> or us=
e:=0A> =A0 =A0 =A0=0A> =0A>=
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ubscribe: =0A> =A0 =A0 =A0=0A>=
 =0A=0A> =0A> Job: =
http://www.ccl.net/jobs =0A> Conferences: http://server.ccl.net/chemistry/a=
nnouncements/conferences/=0A> =0A> Search Messages: http://www.ccl.net/chem=
istry/searchccl/index.shtml=0A> =0A> If your mail bounces from CCL with 5.7=
.1 error, check:=0A> =A0 =A0 =A0=0A> =0A> R=
TFI: http://www.ccl.net/chemistry/aboutccl/instructions/=0A> =0A> =0A> =0A=
=0A=0A


From owner-chemistry@ccl.net Wed Jul  8 16:28:01 2009
From: "patrick o tuck potuck:_:lakeheadu.ca" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL:G: excited state optimizations using TDDFT with gaussian 09
Message-Id: <-39715-090708151227-32583-YViMCDtad6ODvhgJynbLOQ^^server.ccl.net>
X-Original-From: "patrick o tuck" <potuck%x%lakeheadu.ca>
Date: Wed, 8 Jul 2009 15:12:23 -0400


Sent to CCL by: "patrick o tuck" [potuck%a%lakeheadu.ca]
Hello:

SO I am using gaussian 09 and have been fortunate to find a stationary point in the first excited state of a molecule. However, after running a numerical frequency check on it (only numerical is available to my knowledge for excited state TDDFT), it tells me it has one imag. frequency, i.e a Transition state! 

So I corrected the Transition State coordinates to put me close to the minima with no i-freqs, but after running an optimization again, it fails and reads out:

"You need to solve for more vectors in order to follow this state."

My question is what is the significance of this and how to avoid it. Am I on a flat part of the PES, and the software doesn't not where to go, or is there some kind of conical intersection thing happening. A suggestion of a keyword to help find a minima would also be very much appreciated.

Patrick


From owner-chemistry@ccl.net Wed Jul  8 17:36:00 2009
From: "David Mannock dmannock{=}ualberta.ca" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: Question on sterol/lipid interactions and CCL
Message-Id: <-39716-090708155600-5989-blNRsIHn8SsQsCkCYRU5bw%server.ccl.net>
X-Original-From: David Mannock <dmannock_._ualberta.ca>
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Date: Wed, 08 Jul 2009 13:02:54 -0600
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Sent to CCL by: David Mannock [dmannock**ualberta.ca]
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Hi! I do experimental work on lipid/sterol mixtures and have been 
looking at the existing computer calculations and bilayer simulations of 
these mixtures in an effort to interpret thermodynamic and structural 
data. It seems to me that there are a lot of problems in this area. 
Different molecular force fields give disparate pictures, electrostatic 
calculations are performed independently and are not part of the 
conformational calculations. Where steepest descent algorithms are 
employed in conformational analysis, they obtain the global minimum 
energy conformation and those conformations are used in simulations, yet 
they may be only one of several conformations in a dynamic system even 
where there are lateral forces between molecules in the bilayer. There 
is some recent experimental and computer work which seems to acknowledge 
that the alkyl side-chain may be kinked and not fully extended in some 
biological sterols, but these are in the minority and explanations for 
such conformations are weak. Also, contrary to established belief, the 
all-/trans/ polycyclic ring system is not completely inflexible (this is 
even evident in crystal structures) and the conformations of rings A, B 
and D are not the same in all sterols. In fact, the addition of methyl 
groups, changes in functional group chemistry and the insertion of 
double bonds into the ring and side-chain introduce major changes in 
molecular properties. Why are these calculations not detecting this when 
the indications are there in other areas of the sterol and steroid 
literature? Why are the molecular electronic properties not included in 
many conformational analyses prior to the bilayer simulations and why 
are the global minimum energy conformations used in the simulations when 
it might be better to consider the dynamic electrostatic potential 
surfaces? There is some interesting calculations which look at the 
contact surfaces/fingerprints between phospholipids and sterols using MD 
methods. Is anyone doing this kind of analysis on sterols other than 
cholesterol? David Mannock

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>

<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi! I do experimental work on lipid/sterol mixtures and have been
looking at the existing computer calculations and bilayer simulations
of these mixtures in an effort to interpret thermodynamic and
structural data. It seems to me that there are a lot of problems in
this area. Different molecular force fields give disparate pictures,
electrostatic calculations are performed independently and are not part
of the conformational calculations. Where steepest descent algorithms
are employed in conformational analysis, they obtain the global minimum
energy conformation and those conformations are used in simulations,
yet they may be only one of several conformations in a dynamic system
even where there are lateral forces between molecules in the bilayer.
There is some recent experimental and computer work which seems to
acknowledge that the alkyl side-chain may be kinked and not fully
extended in some biological sterols, but these are in the minority and
explanations for such conformations are weak. Also, contrary to
established belief, the all-<i>trans</i> polycyclic ring system is not
completely inflexible (this is even evident in crystal structures) and
the conformations of rings A, B and D are not the same in all sterols.
In fact, the addition of methyl groups, changes in functional group
chemistry and the insertion of double bonds into the ring and
side-chain introduce major changes in molecular properties. Why are
these calculations not detecting this when the indications are there in
other areas of the sterol and steroid literature? Why are the molecular
electronic properties not included in many conformational analyses
prior to the bilayer simulations and why are the global minimum energy
conformations used in the simulations when it might be better to
consider the dynamic electrostatic potential surfaces? There is some
interesting calculations which look at the contact
surfaces/fingerprints between phospholipids and sterols using MD
methods. Is anyone doing this kind of analysis on sterols other than
cholesterol? David Mannock<br>
</body>
</html>

--------------020304020106010908080903--


From owner-chemistry@ccl.net Wed Jul  8 23:24:00 2009
From: "case case~!~biomaps.rutgers.edu" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: pKa calculation of strong acid
Message-Id: <-39717-090708104352-11257-zKZ2nq2dlxFPPPP6KIA1rQ===server.ccl.net>
X-Original-From: case <case(_)biomaps.rutgers.edu>
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Date: Wed, 8 Jul 2009 10:43:38 -0400
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Sent to CCL by: case [case##biomaps.rutgers.edu]

On Tue, Jul 07, 2009, VITORGE Pierre 094605 Pierre.VITORGE^^cea.fr wrote:
> 
> The pKa of a strong acid have no finite value, namely it does not exist.

These values certainly exist.  For the HCl example that was in the
original post, the pKa in aqueous solution is around -6, although this
seems to have a big uncertainty.  You would have to spend some time to
find the original determination -- a secondary reference to start from
would be Albert and Serjeant, "The Determination of Ionization Constants",
Chapman & Hall, 1984.

....dave case