From chemistry-request@www.ccl.net  Tue Aug 11 01:02:09 1998
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Date: Tue, 11 Aug 1998 07:05:08 +0200 (METDST)
From: Thomas Nowak <Nowak@Chemie.UNI-Halle.DE>
Message-Id: <199808110505.HAA00867@mailsrv.rz.fh-merseburg.de>
To: CHEMISTRY@www.ccl.net
Subject: CCL:MM3 parameters




dear all,

i'm looking for suitable parameters for the mm3 force field 
to model organophosphourus(iii) ligands, expecially phosphites
(f.i. trimethyl -> P(OMe)3, triphenyl -> P(OPh)3), but
also phosphines (f.i. trimethyl -> PMe3; triphenyl -> PPh3).
Although the latter should be included in the standard
parametrization, no suitable set of parameters describing the phosphites
are found. I my resarch the TINKER package was used.

Is there anybody out there who can give me some pointers to the needed
parameters or even better, who has made her/his own set of parameters
by hand.

best regards

Thomas


From chemistry-request@www.ccl.net  Tue Aug 11 04:20:29 1998
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From: "Philip Gisdakis" <gisdakis@theochem.tu-muenchen.de>
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To: CHEMISTRY@www.ccl.net
Subject: Visualize NMR Calculations?




Hi everybody,

is there a (free?) tool to simulate a NMR spectra
from calculated (Gaussian) chemical shifts? We want
to use it for educational purposes.

Thank you
Philip

-- 
Philip Gisdakis

      o-----------------------------------------------------------------o
     /        Philip Gisdakis         gisdakis@theochem.tu-muenchen.de / \
    /    Theoretical Chemistry       Phone: +49 +89 289 13618 (Univ.) /   o
   /Technical University of Munich                67908232  (Privat) /   /
  /     Lichtenbergstrasse 4                                        /   /
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From chemistry-request@www.ccl.net  Tue Aug 11 07:12:22 1998
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Subject: Is there a need for a Calculated Structures Database ?
To: chemistry@www.ccl.net
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From: Gijs Schaftenaar <schaft@caos.kun.nl>




A Calculated Structures Database.
---------------------------------

Not more than perhaps a decade ago, Computational Chemistry used to be the 
realm of Quantum Chemists with access to a supercomputer. Computer resources
usually restricted calculations to small molecules. Nowadays this situation 
has changed drastically. With the continuous speedup of computer hardware, 
calculations on chemically interesting systems have become tractable to the 
bench chemist and the study of short lived intermediates and transition 
states, often inaccessible to experiment, have become common practice.
The Computational Chemistry community has steadily grown and broadened 
and does no longer exist of pure specialists only. The Computational 
Chemistry List (CCL; URL: http://www.ccl.net/ccl/welcome.html), a Web 
site and an e-mail exploder which allows computational chemistry researchers 
from around the world to exchange information and experiences is an important 
commucation channel.  

With so many structures being calculated, the need for a (comprehensive) 
database of calculated structures has been voiced a number of times on the 
Computational Chemistry List. The Carnegie-Mellon Quantum Chemistry Archive, 
created by Prof. Pople's group for users of the Gaussian package, has been 
an attempt to set up such a database. However, for a number of reasons this 
database has never been very successful. Gaussian users could (can) contribute
to this database by sending a routinely created archive file by surface 
mail to the curators of the database, the Chemistry Publishing Unit of 
Carnegie-Mellon University. Access to the database can only be obtained by 
purchasing it together with its dedicated software. But for a database to 
be successful, ease of contributing to it and ease of data retrieval are 
determing factors. 

The CAOS/CAMM Center, the Dutch national academic Center for the 
Application of Information Technology in Chemistry, is exploring the 
possibility to create, curate and maintain a comprehensive archive of 
calculated structures at both the ab-initio and semi-empirical level with 
emphasis on co-ordinate data. Contributions to this database should be 
submitable via e-mail and/or the World Wide Web. We intend to automate 
submission by incorporating a submission form into our popular quantum 
chemistry visualisation tool MOLDEN, which interfaces not only to Gaussian 
but to a range of other Ab Initio and semi-empirical codes. MOLDEN currently 
has a distribution of over 800 copies world wide and is freely available to 
academic researchers making (coordinate) data contibution an easy task. 
Access to the database will be given via the World Wide Web and added value 
is intended by linking it to other chemically oriented databases, in 
particular to the Quantum Chemistry Literature Database (QCLDB). 
The Gaussian archive file format might serve as a starting point for the 
definition of a new and richer format which would include semi-empirical 
calculations and links to literature and other chemical databases. Because 
the Center maintains the MOLDEN software, adaptions to deal with a new 
data format can easily be implemented and distributed. 

With this message we try to measure the potential (mental) support for 
such an initiative and to determine the willingness among computational 
chemists to contribute data to the intended database of calculated structures.
This will help us to determine if the allocation of computational and 
human resources to this effort can meet with sufficient enthousiasm to 
start. For the database to reach the critical mass needed to become a 
successful operation, in addition to the processing of existing data sources, 
the active contribution of data from many private sources is necessary. 
Therefor your answer to the following questions is very much appreciated.

1. Do you think that the proposed initiative is advisable and/or needed ? 

2. Would you be willing to contribute data to the proposed database, using
   either a MOLDEN form or a WEB based form?
  

Your answers are welcomed at the e-mail addresses:

schaft@caos.kun.nl (Gijs Schaftenaar, Computational Chemist and MOLDEN 
                    author CAOS/CAMM Center.)
or

noordik@caos.kun.nl (Jan Noordik, Director CAOS/CAMM Center)

------------------+-----------------------+------------------------------
                   CAOS/CAMM Center        Phone:  +31(0)24-3653386
                   University of Nijmegen          +31(0)24-3653391(secr.)
                   Toernooiveld 1          Fax:    +31(0)24-3652977
                   6525 ED Nijmegen        e-mail: post@caos.kun.nl
                   The Netherlands         URL:    http://www.caos.kun.nl
------------------+-----------------------+------------------------------
The CAOS/CAMM Center is the Dutch Academic Facility for the Application of
Information Technology in: 
                          Organic Chemistry:                        CAOS 
         Computational Chemistry, Molecular Modeling, 3D Databases: CAMM 
                          Bioinformatics:                           CAMMSA
             It is also the Dutch National Node in EMBnet and GDB.
------------------+-----------------------+------------------------------

 
  



From chemistry-request@www.ccl.net  Tue Aug 11 10:44:51 1998
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From: "Gert Kruger" <kruger@eng.und.ac.za>
To: chemistry@www.ccl.net
Subject: CCL:G94W on DEC Alpha for NT



Dear CCL,

We are investigating buying either a Digital Personal Workstation for Windows NT or a the equivalent in Unix (www.dec.com).  The NT version is considerably cheaper and the suppliers claim that the two machines perform equal.

Gaussian however, does not supply a version for Alpa NT machines, and one would have to use additional software (which is standard with NT 5) in order to run normal NT software.

I would appreciate any comments on:
1.  The performance of the 2 machines.
2.   The use of Gaussian for Windows software on the DEC Alpha machine.  How does it compare with the Unix software.
3.  Any other hints.

I will summarise the info.
Best wishes
Gert Kruger

___________________________________
Dr HG Kruger, Chemistry, University of Natal 
P.O. box 18091, Dalbridge 4014
Durban, South Africa.
tel: +27-31-2603090   fax: +27-31-2603091
email: kruger@scifs1.und.ac.za
___________________________________



From chemistry-request@www.ccl.net  Tue Aug 11 13:32:27 1998
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Date: Tue, 11 Aug 1998 13:32:26 -0400 (EDT)
From: "E. Lewars" <elewars@alchemy.chem.utoronto.ca>
Message-Id: <199808111732.NAA26595@alchemy.chem.utoronto.ca>
To: chemistry@www.ccl.net
Subject: NEG ACTIV E: SUMMARY




Tuesday 1998 August 11

Hello,

Thanks to all who replied to my question about negative activation energies:
P-O Norby, A. Korkin, S. Abrash, M. Hohmann, J. Vill'ai Fre, l. Burke,
A. Shusterman and J. Perry (I hope I haven't missed any one).

The question was:

Sometimes one gets a _negative_ value for an activation E.  For example

                  O               O
                   \\              \\...
                    C---O           C---O
                    |   |  ----->   .   . transition state   --> CO2 + N2
                    N===N           .   .
                                    .....
                                    N====N
                -297.56194 h
                                     -297.56281 h

      activ E = -0.00087 h = -2.28 kJ/mol     G2(MP2) energies

 Sometimes one gets a negative value with and without the ZPE corection.


 Is there any special theoretical significance to such "impossible"
activation E's?  Or can one just say that (since not much below zero) they
are compatible with a low positive barrier?

     Thanks

              E. Lewars
==============

I now see that -ve activation E's can easily be obtained if the barrier is low;
they are essentially just errors caused by errors in the ZPE, or, in the case
of single-point calcs on a structure optimized at a lower level (which is
what G2-type calcs are), errors can arise from the fact that the lower-level
statonary points will not be exactly the max and min on the higher-level PES.
                    .
                  .   .
      .         .x      .                     x
        .     .  |       .                    |
          .. .   |        . .~.               | -ve       ~
        .        |       . ./|\ .             |          /|\
         .      \|/    .    .|    .          \|/          |
           .     ----------- x      .         x           |  +ve
              .     .        |.       .                   |
                . .  ________|_.        .                 |
                 ~              .                         ~
                                 .


 I think this is the cause in this case; as others pointed out (SUMMARY BELOW),
there can be other causes of neg activ E's, like precomplexation (van der Waals
complexes) and etc (J Chem Phys, 1997, 107, 7266), and when the
Arrhenius A factor dominates the exponential factor (deltaE ~- 0).

------------
SUMMARY OF RESPONSES:


                  3-AUG-1998 17:36:45.52
>From:  IN%"peon@medchem.dfh.dk"  "Per-Ola Norrby"
To:     IN%"elewars@alchemy.chem.utoronto.ca"  "E. Lewars"
Subj:   CCL:NEGATIVE ACTIVATION E's


        Well, in this case, it just means you use an improper method...
The G2 methods are extrapolation methods that depend on the geometry being
well represented by a low level method.  In this case, you are using
HF/6-31G* to locate the TS geometry, I guess this is the source of your
problem.  If you use a method where you calculate the energy at the same
level as your geometry, this type of problem should disappear (there are
other possible sources of apparent negative TS energies, like
precomplexing, but that should not apply in your case).  For some good
possible choices for geometry optimization levels, I'd suggest
MP2/6-311G**, or B3LYP/6-31G* (depending on your computational resources
and/or theological leaning).

        The G2 methods were developed to calculate VERY accurate heats of
formation, but in general, I wouldn't recommend them for TS calculations
(just a personal opinion, I'd like to hear if there is a concensus on this).

        Regards,

        Per-Ola Norrby

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Per-Ola Norrby, peon@medchem.dfh.dk
Royal Danish School of Pharmacy, Dept. of Med. Chem.
Universitetsparken 2, DK-2100 Copenhagen, Denmark
Tel: +45-35376777-506, +45-35370850, fax +45-35372209
=============



>From:  IN%"r40757@email.mot.com"  "Anatoli Korkin"
To:     IN%"elewars@alchemy.chem.utoronto.ca"  "E. Lewars", IN%"chemistry@infome
ister.ccl.net"  "chemistry@www.ccl.net", IN%"bartlett@qtp.ufl.edu"  "Rod
 Bartlett"
Subj:   CCL:NEGATIVE ACTIVATION E's

Negative activition energies you may get in two cases (may be someone
knows more): 1) There is an intermediate complex between reagents and 
a TS. In this case everything is "normal". Some SN2 gas phase 
reactions have "negative" activitations energies. This led first to a
suspecion among experimentalists, who studied these reactions in
solutions,
that theory was wrong, but later this result has been confirmed for
gas phase reactions. 2) For very low barriers you may get negative
activation energies, if you do (higher level) single point calculations
using geometries optimized at another (lower correlation) approach.
If you optimize a TS and reagents at the same level and there is
no an intemediate mimimum on a reaction pathway you should not get
your electronic energy for TS lower than that one for reagents. Of
course, zero point energy correction may change the sign of the barrier,
if it is very small (e.g. 1 kcal/mol or lower). Anyway at such low
barriers a conventional transition state theory is hardly applicable,
and a dynamical treatment is required.

Regards,

Anatoli

P.S. We have a paper on CN2O2 species including the complex below.
An activation energy we got at CCSD(T)/TZP//MBPT(3)/6-31G* was 0.5
kcal/mol before and -0.3 kcal/mol after ZPE correction.
-----------

******************************************************************

Anatoli A. Korkin, Ph.D         Predictive Engineering Lab
Computational Chemist           Semiconductor Products Sector
Motorola Inc., MD M360          Tel:    (602) 655-3171
2200 W. Broadway Road           Fax:    (602) 655-5013
Mesa AZ 85202                   E.mail: r40757@email.mot.com
                                        
*******************************************************************



X-Sender: sabrash@facstaff.richmond.edu
Subject: Re: CCL:NEGATIVE ACTIVATION E's

Dear Professor Lewars,
        I cannot give you the answer for the theoretical case, but can explain t
he
significance for experimentally determined negative activation energies.

The rate constant for a reaction in the Arrhenius model is given by k =
A(T) exp (-Ea/RT).  Because the activation energy temperature dependence
typically swamps that due to the preexponential factor, typical Arrhenius
analyses ignore the temperature dependence of the A term.  However when Ea
is for all practical purposes zero, then the temperature dependence is that
of the A factor which tends to increase with decreasing temperature.  This
therefore appears as a negative activation energy.  Such reactions are
better fit by the equation

  k = AT^m exp(-E0/RT), where E0 is equivalent to the zero k activation energy.

Best regards, 

Sam Abrash

>==============
Sam Abrash
Associate Professor
Department of Chemistry
University of Richmond
Richmond, VA  23174
(804) 289-8248
Fax: (804)289-8482
sabrash@richmond.edu

"I believe in the open mind, but not so open your brain falls out."
==================



Subject: neg. E act
To: elewars@alchemy.chem.utoronto.ca
Date: Mon, 3 Aug 1998 15:10:42 -0500 (EDT)
X-Mailer: ELM [version 2.4 PL20]

Hi!

Negative activation energies can result
- from ZPE corrections or
- if you derive your relative energies from single point calculations
  and the geometries used are not good enough (i.e. the geometries at the
  level of opt and at the level of single points deviate considerably) 

If you get a "neg. activation energy" at the level of geometry opt., 
something is wrong. I suggest to look at the vector of the imaginary frequency 
first. If it seems to be ok check the transition state with
an IRC (intrinsic reaction coordinate) calculation. 

Good luck,
Matthias       M. Hohmann
============



Jordi Villa i Freixa
Department of Chemistry
University of Southern California
Los Angeles, CA, USA, 90089-1062 
Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701
villa@mutant.usc.edu      http://t1.chem.umn.edu/~villa



-What you call "activation energy" is, in fact, an energy barrier. 
Activation energy is a kinetic concept that comes from the Arrhenius 
equation.

-Probably the small negative value you obtain is due to the G2 method,
where you are not exploring exactly a concrete potential energy surface, 
but adding the contributions of several corrections to the initial energy 
surface. 

-The example you are posting is really interesting because of the low 
barrier (in your case is negative, but I guess that using only the
non-G2-corrected surface the barrier would be positive or zero). This 
means that considering the barrier to be the given value could lend you 
to an error when trying to understand kinetic experimental results, for 
example. The location of only the saddle point on this reaction will not 
be enough to understand the dynamics of the system, and a treatment with 
variational transition state theory could be necessary.

If you want more information about the dynamic treatment of this kind of 
barrierless or almost barrierless reactions take a look to:

J. Chem. Phys. 1997, 107, 7266
J. Am. Chem. Soc. 1998, 120, 5559.

I hope this will help

Yours

Jordi
===========


          Aug 3  Luke A. Burke      (31)   impos tsCommand: Read MessageMessage 5/17 from Luke A. Burke                           Aug 3 '98 at 6:59 pm

Date: Mon, 3 Aug 1998 18:59:03 -0400
X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail)
To: elewars@alchemy.chem.utoronto.ca
Subject: impos ts
Mime-Version: 1.0

 ...............

If your structure is indeed a ts, then there must be a minimum and another ts
between your drawn structures. You did not give the geometry of the ts but I
suspect that there is the involvement of van der Waals complexes.
BTW, in the history of ts oddities, I found a reaction (rotation) where the Ea
>0, but Ha<0 and Ga<0.

Salut, de koste en de wind van achter, en de steenweg tot huis toe (plat
Leuvense)

Luke

-- 
Luke Anthony Burke              tel:609-225-6158 (-6142)
Professor and Chair,            fax:609-225-6506
Rutgers University              burke@camden.rutgers.edu
Camden, NJ 08102, USA           http://camchem.rutgers.edu/~burke
==============



Alan Shusterman
Date: 03 Aug 98 13:42:35 PDT
Subject: Re: CCL:NEGATIVE ACTIVATION E's

I noticed that your negative barrier results from comparison of =
G2(MP2) energies. I'm not very familiar with the G2 model, but I =
was wondering what model was used to identify the reactant minimum =
and transition state, and did this model give a negative or =
positive barrier?

Alan
----------------
Alan Shusterman
Department of Chemistry
Reed College
Portland, OR
www.reed.edu/~alan
==============================


           Aug 3  Jason K. Perry     (31)   Re:  CCL:NEGATIVE ACTIVATION E'sCommand: Read MessageMessage 8/17 from Jason K. Perry                          Aug 3 '98 at 1:53 pm

Date: Mon, 3 Aug 1998 13:53:36 -0700 (PDT)
To: "E. Lewars" <elewars@alchemy.chem.utoronto.ca>
Subject: Re:  CCL:NEGATIVE ACTIVATION E's

> Sometimes one gets a negative value with and without the ZPE corection.

The reason you're seeing negative activation energies is because with the
G2 method you are calculating the geometry at one level and reporting
an energy at a different level.  At the level that the geometry was
determined it is most certainly the case that the activation barrier
is positive.  For example, if I calculate geometries for reactant, product
and transition state at the HF/6-31G** level, the transition state will
be correct for that level and show a positive barrier.  If I then do
single point B3LYP/6-31G** calculations using those HF/6-31G** geometries
the transition state will not be correct for the new level, and
thus there is no guarantee that the barrier will be positive.

        Jason Perry
        First Principles Research, Inc.
================


From chemistry-request@www.ccl.net  Tue Aug 11 17:51:40 1998
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Date: Tue, 11 Aug 1998 16:38:27 -0500 (CDT)
From: Nathalie Godbout <godbout@chad.scs.uiuc.edu>
To: chemistry@www.ccl.net
cc: "Prof. Eric Oldfield" <eo@chad.scs.uiuc.edu>
Subject: G94 cube file units and Cerius2
Message-ID: <Pine.A41.3.95.980811163647.16142B-100000@chad.scs.uiuc.edu>







    Dear computational chemists,


     I have a question concerning electron density surfaces 
calculated with G94 (cube=density), the use of Cerius2 to
display these surfaces and units. 

     According to the cube file I have calculated, the density
values range from 0 to 27 electrons/bohr^3 (I think). When I
use the Gaussian interface in Cerius2 to display the surface,
the property range displayed is 0 to 182. Using the conversion 
factor between electrons/bohr^3 and electrons/angstrom^3 (6.75),
I get the the property range displayed in Cerius2. To make sure
this was correct, I created a 3X3X3 cube with only one non-zero value, namely 1.0.
When I display this cube in Cerius2, I expected the property to range
from 0 to 6.75 e/A^3. I get that the range is 0 to 1.0. Further, I am
able to display electron density values between 0.0 and 1.0. 

    Are the values in the cube file multiplied by a conversion factor
or are values extra/intrapolated?

   I have also the same question for the electrostatic potential for which
there is also a difference the cube file values and the displayed
values. 

   I will summarize.

   Thank you for your help.

       
       Nathalie


 --------------------------------------------
| Nathalie Godbout                           |
| University of Illinois at Urbana-Champaign |
| 600 S. Goodwin Av. Box 23.6                |
| Urbana, IL 61801                           |
 --------------------------------------------



From chemistry-request@www.ccl.net  Tue Aug 11 18:36:49 1998
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From: "Artiben Taylor" <ihtrap@hotmail.com>
To: chemistry@www.ccl.net
Subject: Optimization problem
Date: Tue, 11 Aug 1998 15:36:19 PDT



I am trying to optimize a structure with opt=(tight,maxcyc=100).
But the geometry is not converging. After 4 converging point
it comes back to the original point.
         Item               Value     Threshold  Converged?
 Maximum Force             .000018      .000015     NO
 RMS     Force             .000008      .000010     YES
 Maximum Displacement      .009113      .000060     NO
 RMS     Displacement      .003305      .000040     NO
Kind of trapped in a loop. I tried to reoptimize the geometry
by changing little. But it doesnt help. In another probelm,
I am getting YES flags for the optimization but in the frequency
calculation I am getting the RMS as NO. I would appreciate
to receive your comments. Thanks. Artiben.

______________________________________________________
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From chemistry-request@www.ccl.net  Tue Aug 11 21:45:46 1998
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Subject: CCL:Valence DOS calculations
To: chemistry@www.ccl.net
Date: Wed, 12 Aug 1998 09:45:43 +0800 (SST)
From: "Chin Wee Shong" <chmcws@leonis.nus.edu.sg>
Cc: chmcws@leonis.nus.edu.sg (W S Chin)



Dear CCLers,

I am looking at ways/programmes to calculate the density of states
for some simple organic molecules in order to correlate that to their 
valence electronic structures.  Can someone please give your kind 
advice or pointers ?

Regards,
Lim S L
e-mail:scip4160 @ leonis.nus.edu.sg


