Subject: Summary of my earlier questions, answers & thanks(part 2 of 3)

From: "Park, Tae-Yun" <[email-masked]>
Date: Thu, 1 Aug 1996 13:01:43 +0200 (DFT)

-------------------------------------------------------
PART III
      Subject: Transition state search using MOPAC.
-------------------------------------------------------
####################(questions)########################

Dear all,

I need some help from people who uses MOPAC frequently,
as I'm a real beginner of using MOPAC.

I want to search the transition state(TS) of the following 
reaction with MOPAC93:

   H              H     H                       H H H
   |               \   /                        | | |
 H-C(+)       +     C=C     ---->(TS?)---->   H-C-C-C(+)
   |               /   \                        | | |
   H              H     H                       H H H

 gas-phase                                     gas-phase
   methyl         ethylene                   primary propyl
carbenium ion                                 carbenium ion

After reading the session of transition state location(SADDLE) 
in MOPAC manual, I have prepared the following input data for 
MOPAC:

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

UHF  SADDLE DENSITY GRAPH XYZ CHARGE=1 BAR=0.03 
Me--->p methylation activated complex

 C     .000000 0     .000000 0     .000000 0       0    0    0
 H    1.113983 1     .000000 0     .000000 0       1    0    0
 H    1.113983 1  120.001495 1     .000000 0       1    2    0
 H    1.113968 1  119.999756 1 -179.453217 1       1    2    3
 C    5.210007 1  129.371857 1 -179.367538 1       1    2    3
 C    1.336975 1  114.626526 1   -2.741700 1       5    1    2
 H    1.099976 1  120.501572 1 -179.999634 1       5    6    1
 H    1.100006 1  119.749710 1 -179.453217 1       5    6    7
 H    1.099976 1  120.499832 1  179.999634 1       6    5    7
 H    1.099976 1  119.749710 1     .547287 1       6    5    7
 0    0.000000 0    0.000000 0    0.000000 0       0    0    0
 C     .000000 0     .000000 0     .000000 0       0    0    0
 C    1.506600 1     .000000 0     .000000 0       1    0    0
 C    1.418946 1  116.679237 1     .000000 0       2    1    0
 H    1.118213 1  111.091591 1  -60.563965 1       1    2    3
 H    1.119848 1  109.781792 1  179.985870 1       1    2    3
 H    1.118203 1  111.102783 1   60.532600 1       1    2    3
 H    1.150792 1  110.664017 1  174.500137 1       2    1    4
 H    1.150722 1  110.665337 1   64.389313 1       2    1    4
 H    1.109605 1  121.234596 1  179.993790 1       3    2    1
 H    1.110235 1  121.565987 1    -.003556 1       3    2    1
 0    0.000000 0    0.000000 0    0.000000 0       0    0    0

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

The result with this input data was terrible; in the transition 
state, H2 and H were separated!

The data were prepared as follows:

1. I've drawn two reactants using CS Chem 3D Pro and save as 
   MOPAC input.  I could not optimize the geometry of these
   two molecules in MOPAC simulatneously, since there are two 
   molecules exist.

2. The data for the product carbenuim ions was prepared 
   with CS Chem3D Pro again, and the geometry of this 
   molecule was minimized with MOPAC keywards, 
    
      "SYMMETRY CHARGE=1 AM1 GEO-OK EF PRECISE"

   and then saved as an optimezed data for the product 
   carbenium ion.

3. Then I combined these two files and modified according 
   to the decription in the MOPAC manual for SADDLE 
   calculation.

4. And I've got the terrible result.

What's wrong with my input data for the SADDLE calculation?
Is it really possible to get the optimized geometry of 
transition state for the reaction I mentioned above by 
using MOPAC?  

If so, could anyone PLEASE tell me how I can get a reliable
structure of the transition state theoretically?

ANY suggestion/advice will be GREATLY APPRECIATED!

Thank you very much in advence.

####################(Answers)########################

From [email-masked] Jul 27 11:07:03 1996
Date: Tue, 9 Jul 1996 21:32:47 -0600
From: Emadeddin Tajkhorshid <[email-masked]>
Reply to: [email-masked]
To: "Park, Tae-Yun" <[email-masked]>
Subject: Re: CCL:M:Transition state search using MOPAC.

Hi Tae-Yun

As far as I exprienced MOPAC, you should use the same order of atoms in your
input file for the geometry of reactants and products. Otherwise you will find
a nonsense result. Because MOPAC tries to reconstruct the reaction coordinate
toward saddle point via considering the satrting and ending geometry of each
atom and is not able to automatically find the right counterpart in the second
strusture. On the other hand it is recommended to use XYZ key word even if you
use internal coordinate. This can prevent some kind of special errors which may
occur in this routine

Good luck
Emad

-- 
E. Tajkhorshid				
German Cancer Research Center; DKFZ	Tel: +49 6221 42 2339
Dept. Molecular Biophysics (0810)	FAX: +49 6221 42 2333
P.O.Box 101949				Email: [email-masked]
69009 Heidelberg, FRG
**********************************************************************
* It is nice to be important, but it is more important to be nice!   *
**********************************************************************

From lldmpc::mrgate::a1::[email-masked] Jul 27 11:07:45 1996
Date: Tue, 9 Jul 96 16:18:10 EDT
From: "lldmpc::mrgate::a1::moralega"@lldmpc.dnet.dupont.com
To: [email-masked]
Subject: RE: CCL:M:Transition state search using MOPAC.

From:	NAME: GUILLERMO A. MORALES          
	FUNC: Research and Development        
	TEL: 695-1053                         <MORALEGA@A1@LLDMPC>
To:	NAME: [email-masked] <"[email-masked]"@ESDS01@MRGATE@LLDMPC>

Hi Tae-Yun,

I've located transition states for Diels-Alder reactions using CS Chem 3D Pro 
and MOPAC. I haven't done any work with carbocations, though.
Anyways, this is the method I used. Check it out and compare it with yours.

1) Using CS Chem 3D Pro build first the expected product and minimize it.
2) Check that the atom numbers are continuous (1,2,3,etc.). If for some reason 
one is skipped then renumber ALL the atoms manually (check the manual on how to 
do this).
3) Save the molecule in MOPAC format.
4) Now with the pointer selec the CH3 unit on the far left (like when you do 
cut/paste in windows), drag it to the left side of the screen and delete the C-C 
bond. This is going to be your CH3+ ion.
5) The rest of the molecule is going to be converted automatically into CH3-CH3
   Make it manually CH2=CH2
6) I think if you select the CH2=CH2 with the pointer you can minimiza ONLY that 
molucule EVEN THOUGH the CH3+ is present. I'm not really sure of this.
7) BEFORE you save this window as a MOPAC file MAKE SURE the atom numbers ARE 
THE SAME. In other words, if in the CH3+ the C is atom 1, then the other H are 
2,3,4 MAKE SURE in the expected product the carbon on the left is atom 1 and 
it's corresponding Hs ae 2,3 and 4. Same fopr the CH2=CH2 unit. This step is 
CRUCIAL for the saddle calculation since the connectivity in starting materials 
MUST BE the same as in final products.

8) Now combine both MOPAC files the way you did it before, include the 
appropriate keywords and run the calculations.

9) Even if the final geometry is not the real transition state (thing I doubt), 
then take the generated final geometry and refine it. This should do the trick.

If you have any more questions just let me know, OK?

Good luck.

Guillermo.
-------------------------------------------------------------------------------
Guillermo A. Morales, Ph.D.
Postdoctoral Fellow
The DuPont-Merck Pharmaceuticals Co.
-------------------------------------------------------------------------------
Note: The ideas/comments herein expressed are mine only. 

From [email-masked] Jul 27 11:11:41 1996
Date: Tue, 9 Jul 1996 16:45:36 -0400 (EDT)
From: Stanislaw Oldziej <[email-masked]>
To: [email-masked]
Subject: Transition state:

Hi,

1. You should remember that order of atoms in substrate compex and in 
products should be identical. If you see in substrate atom 2 it is 
hydrogen in products it is carbon ect. 

2. Why you using UHF ?

With best regards

Stanislaw Oldziej

From [email-masked] Jul 27 11:12:46 1996
Date: Tue, 9 Jul 1996 17:30:25 -0400
From: Bill Laidig <[email-masked]>
To: "Park, Tae-Yun" <[email-masked]>
Subject: Re: CCL:M:Transition state search using MOPAC.

Tae-Yun,

I would do this calculation as follows since I do not know what the TS will
look like in advance. I would optimize the geometry of the product ion
first. Next, I would do a series of constrained minimizations in which the
CH3-C2H4+ r(C-C) was systematically stretched (i.e. the first calculation has
r(C-C) at the equilibrium distance (re), next fixed at re+0.1, next fixed at
re+0.2... After a maximum along the stretching coordinate was located, I
would next use this geometry unconstrained in a TS calculation. Bill

-- 
******************************************************************************
*    "Like jewels in a crown, the precious stones glittered in the queen's   *
*     round metal hat." - Jack Handey                                        *
*                                                                            *
*     Bill Laidig                                                            *
*     The Procter & Gamble Co.             tel 513-627-2857 fax - 1233       *
*     Miami Valley Laboratories            [email-masked] (preferred)         *
*     P.O. Box 538707                      [email-masked]                  *
*     Cincinnati, OH 45253-8707            [email-masked]                *
******************************************************************************

From [email-masked] Jul 27 11:13:31 1996
Date: Wed, 10 Jul 1996 01:21:48 +0200
From: [email-masked]
To: [email-masked]
Subject: M: SADDLE

First, the SADDLE command does not give an optimized geometry of the TS -- only
an approximate geometry.  The "best" TS approximation must be refined using the
TS keyword, or NLLSQ, or some combination (perhaps in several steps), followed
by a FORCE calculation to assure you are at a TS (one -ve root to the Hessian),
and ideally followed by reaction coordinate calculations (IRC=1 and IRC=-1) to
generate the product and starting material.  Only through all this work can you
assure you have a TS for the reaction you are interested in.  This applies to
all TS, incidentally, whether you generate them by the SADDLE command or by
guessing.

Since your results are so spectacularly strange, it seems most likely that your
starting geometry for the separate pieces is indigestible.  I would do some
minimization in Mopac on the starting side before trying the saddle calculation.
I expect there are several "reasonable" geometries for this, and you might have
to try several before you get it right.

Given a "reasonable" starting geometry, you might try running the calculation in
AMPAC, if you have access to the program.  I believe the algorithm for locating
TS is different from that used in Mopac, but the two programs should give
otherwise very similar results (with minor modification, the AMPAC output can be
transferred to Mopac as well).  I think the keyword is CHAIN.

sb

From [email-masked] Jul 27 11:14:17 1996
Date: Wed, 10 Jul 96 9:22:32 METDST
From: Jose Ignacio Garcia <[email-masked]>
To: [email-masked]
Subject: SADDLE calculation

My guess for your problem is that the "terrible" result you get is mainly
due to the fact that you are trying to calculate an ion-molecule reaction
IN THE GAS PHASE. As ions are VERY unstable in the gas phase, its reactivity
can be also very different that that observed in solution, where the ion
is comfortably solvated. Thus, in general, in an isolated system calculation
as yours, an ion always will tend to be "solvated" by the neutral molecule,
through a polarisability mechanism, and will approach to its hydrogen atoms.
Often, this approach ends with a hydrogen abstraction reaction, as you 
observed. I have not experience with cation reactions, but this is exactly
what happens with the paradigmatic SN2 reaction between chloride ion and
methyl chloride. If one wants to correctly describe the SN2 attack, one
must be careful in designing the chloride approach trajectory.
Maybe the inclusion of solvation effects through a continuum model would
help to fix this problem.
I hope this helps you.
Best regards.

Jose I. Garcia

--
--------------------------------------------------------------------------------
Dr. Jose Ignacio Garcia-Laureiro                     Phone : 34-(9)76-762077
Departamento de Quimica Organica                                      761210
Instituto de Ciencia de Materiales de Aragon         Fax   : 34-(9)76-761159
C.S.I.C.-Universidad de Zaragoza                     e-mail: [email-masked]
E-50009 ZARAGOZA (SPAIN)                                     [email-masked]
                                                             [email-masked]
--------------------------------------------------------------------------------
"And all this science I don't understand it's just my job five days a week..."

                                               ELTON JOHN - Rocket man
--------------------------------------------------------------------------------

From [email-masked] Jul 27 11:15:07 1996
Date: Wed, 10 Jul 1996 09:40:09 +0200 (MDT)
From: Hens Borkent <[email-masked]>
To: [email-masked]
Subject: mopac ts calc.

Dear Tae-Yun Park,

Your question is a rather frequent one these days, so
at our site we have developed a tutorial on this subject:
http://www.caos.kun.nl/~borkent/compcourse/comp.html
You can also have a look at the Re-view pages for more 
suggestions:
http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/
In your case it boils down to drawing the product, then
increase the reaction bond length gradually, in which you
should observe a maximum, optimize this conformation using
the keyword TS, check frequencies with FORCE.
I'll give it a try as well.
Sincerely,
-- 

  *****    J.H. (Hens) Borkent, CAOS/CAMM Center,
 *CAOS *   P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
*   /   *  Tel 0031 24 36 52137  Fax 0031 24 36 52977
 * CAMM*   e-mail: [email-masked]
  *****    http://www.caos.kun.nl/staff/borkent.html

From [email-masked] Jul 27 11:15:38 1996
Date: Wed, 10 Jul 1996 11:14:33 +0200
From: Ernst Wallenborn <[email-masked]>
To: [email-masked]
Subject: Re: Transition state search using MOPAC.

Hi tere,

i guess your MOPAC input is corrupt. See:

UHF  SADDLE DENSITY GRAPH XYZ CHARGE=1 BAR=0.03 
Me--->p methylation activated complex

 C     .000000 0     .000000 0     .000000 0       0    0    0
             ^^^^^
a zero here means "do not optimize this coordinate". This
is what you want for 6 coords (since you have 3N-6 degrees
of freedom), but not more. Here's already three of them.
 H    1.113983 1     .000000 0     .000000 0       1    0    0
 H    1.113983 1  120.001495 1     .000000 0       1    2    0
six zeroes so far, including this one. Now the spatial
position of your complex is fixed. Any more zeroes will distort
the result.
 H    1.113968 1  119.999756 1 -179.453217 1       1    2    3
 C    5.210007 1  129.371857 1 -179.367538 1       1    2    3
 C    1.336975 1  114.626526 1   -2.741700 1       5    1    2
 H    1.099976 1  120.501572 1 -179.999634 1       5    6    1
 H    1.100006 1  119.749710 1 -179.453217 1       5    6    7
 H    1.099976 1  120.499832 1  179.999634 1       6    5    7
 H    1.099976 1  119.749710 1     .547287 1       6    5    7
 0    0.000000 0    0.000000 0    0.000000 0       0    0    0
First of all, what's Oxygen doing here in the first place.
You gave it a bond distance of 0.00 not to be optimized, to
atom 0. This cannot lead to any sensical results. 
 C     .000000 0     .000000 0     .000000 0       0    0    0
This is even worse. Now you have two atoms, on a non-defined position
in space, which do not belong there anyway, and which cannot
be moved!
 C    1.506600 1     .000000 0     .000000 0       1    0    0
 C    1.418946 1  116.679237 1     .000000 0       2    1    0
 H    1.118213 1  111.091591 1  -60.563965 1       1    2    3
 H    1.119848 1  109.781792 1  179.985870 1       1    2    3
 H    1.118203 1  111.102783 1   60.532600 1       1    2    3
 H    1.150792 1  110.664017 1  174.500137 1       2    1    4
 H    1.150722 1  110.665337 1   64.389313 1       2    1    4
 H    1.109605 1  121.234596 1  179.993790 1       3    2    1
 H    1.110235 1  121.565987 1    -.003556 1       3    2    1
 0    0.000000 0    0.000000 0    0.000000 0       0    0    0

I guess you mistake was using Chem3D as z-matrix generator.
Try to save as xyz file and read this into mopac (you'll have
to manually edit the input file, naturally). Or settle for
a different z-matrix editor altogether (i use molden, cause
it's unix, free and gives good control over the actual variables)

Hope this helps.

-- 
-ernst wallenborn.

i'm not a bug.
i'm an undocumented feature.

From [email-masked] Jul 27 11:16:34 1996
Date: Wed, 10 Jul 96 14:14:42 METDST
From: Jose Ignacio Garcia <[email-masked]>
To: [email-masked]
Subject: SADDLE calculation

Hello! It's me again. Have you tried to use an alternative method to SADDLE?
For instance, a reaction coordinate can be estimated by starting from the
product and breaking the C-C bond. As the C-C distance increases, the total
energy will change, and a maximum will probably appear. The structure
corresponding to this maximum can be then used as an starting point for a
TS or NLLSQ calculation.
By the way, I am still concerned with solvation. It is sure that in the
approach of the cation to the neutral molecule, an energy minimum
corresponding to an ion-molecule pair will be observed.
Best regards.

Jose I. Garcia
--
--------------------------------------------------------------------------------
Dr. Jose Ignacio Garcia-Laureiro                     Phone : 34-(9)76-762077
Departamento de Quimica Organica                                      761210
Instituto de Ciencia de Materiales de Aragon         Fax   : 34-(9)76-761159
C.S.I.C.-Universidad de Zaragoza                     e-mail: [email-masked]
E-50009 ZARAGOZA (SPAIN)                                     [email-masked]
                                                             [email-masked]
--------------------------------------------------------------------------------
"And all this science I don't understand it's just my job five days a week..."

                                               ELTON JOHN - Rocket man
--------------------------------------------------------------------------------

From [email-masked] Jul 27 11:18:10 1996
Date: Wed, 10 Jul 1996 14:38:10 +0200 (MDT)
From: Hens Borkent <[email-masked]>
To: [email-masked]
Subject: M:Searching transition state 

Dear T-Y Park,

As promised I had a look at your molecule and found
that there is a complication in the form of a cyclic
intermediate, which is more stable than the product.
Furthermore it is possible that you find no TS,
because in vacuum the methyl cation is high in energy
and the energy is falling if it approaches the ethylene,
continuously.
So in fact you have to explore the pot.energy surface
by varying the C-C distance and the C-C-C bond angle.
There is probably a TS between the bridged intermediate
(CH3 symmetrical above the ethylene) and the propyl
cation. This is in fact a corner-protonated cyclopropane.
This system must have been studied in the literature,
using ab initio methods as well. (Von Schleyer, JACS,
early 80's).
Best regards,
-- 

  *****    J.H. (Hens) Borkent, CAOS/CAMM Center,
 *CAOS *   P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
*   /   *  Tel 0031 24 36 52137  Fax 0031 24 36 52977
 * CAMM*   e-mail: [email-masked]
  *****    http://www.caos.kun.nl/staff/borkent.html

From [email-masked] Jul 27 11:18:48 1996
Date: Wed, 10 Jul 1996 15:05:18 +0200 (MDT)
From: Hens Borkent <[email-masked]>
To: [email-masked]
Subject: c3h7+ reference

As a follow-up on my previous mail: the reference is
JACS 103, 5649 (1981)
-- 

  *****    J.H. (Hens) Borkent, CAOS/CAMM Center,
 *CAOS *   P.O. Box 9010, 6500 GL Nijmegen, The Netherlands
*   /   *  Tel 0031 24 36 52137  Fax 0031 24 36 52977
 * CAMM*   e-mail: [email-masked]
  *****    http://www.caos.kun.nl/staff/borkent.html
  Please notice change in the Tel/Fax numbers: 80 -> 243

From [email-masked] Jul 27 11:20:04 1996
Date: Wed, 10 Jul 1996 16:51:24 +0200
From: [email-masked]
To: [email-masked]
Subject: Mopac ts

I would try moving the starting structures closer together, so that the
reactants "look" more like a ts.  The c-c bond length in the ts is (at a guess)
on the order of 1.8 - 2.0 A -- try 2.2 - 2.4 A.

You may also have to simply guess the ts structure, and then refine using TS,
NLLSQ, etc.  it will be _crucial_ in this case that you do the IRC calculations
to assure you have a ts for the desired reaction.

sb

From [email-masked] Jul 27 11:20:14 1996
Date: Wed, 10 Jul 1996 09:48:28 -0500 (CDT)
From: Christopher J Cramer <[email-masked]>
To: [email-masked]
Subject: Re: CCL:M:Searching transition state with MOPAC; part2

   What makes you think there IS a transition state structure? In the gas
phase, I would expect this reaction to have a good chance of being
barrierless. Rather than attempt to locate a TS structure a priori, you might
simply do constrained optimizations pulling off the methyl group by 0.1
angstrom increments (for instance). If you generate a reaction path without a
barrier, you will know that it is fruitless to look for a TS. On the other
hand, if you do find a barrier, you will know where to start your TS
optimization.

CJC

-- 

Christopher J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. SE
Minneapolis, MN 55455-0431
--------------------------
Phone:  (612) 624-0859 || FAX:  (612) 626-7541
[email-masked]
http://pollux.chem.umn.edu/~cramer

-------------------------------------------------------
PART IV
      Subject: Searching transition state with MOPAC; part2
-------------------------------------------------------
####################(questions)########################

Dear all,

I've received a lot of helpful messages from many CCLers, 
concerning my earlier questions on how to get the structure 
of transition state of the reaction,

   H              H     H                       H H H
   |               \   /                        | | |
 H-C(+)       +     C=C     ---->(TS?)---->   H-C-C-C(+)
   |               /   \                        | | |
   H              H     H                       H H H

 gas-phase                                     gas-phase
   methyl         ethylene                   primary propyl
carbenium ion                                 carbenium ion

Thanks a lot! I greatly appreciate all the messages concerning 
this problem. 

Most of the messages pointed out that I made a mistake to prepare
the input file for SADDLE calculation; all the atom should be in
the same order between reactants and product z-matrix field.

I made second try with a corrected input file as follows;

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

SADDLE DENSITY GRAPH XYZ CHARGE=1 PRECISE
Me--->p methylation activated complex

C    0.000000  0    0.000000  0    0.000000  0    0   0   0
C    8.471619  1    0.000000  0    0.000000  0    1   0   0
C    1.325912  1  162.328125  1    0.000000  0    2   1   0
H    1.108597  1   65.592545  1 -150.347214  1    1   2   3
H    1.113968  1  120.001495  1 -151.401566  1    1   4   2
H    1.108612  1  119.996246  1 -179.367538  1    1   4   5
H    1.098282  1  122.722214  1   57.159393  1    2   3   1
H    1.098328  1  122.715210  1  179.999634  1    2   3   7
H    1.098267  1  122.715210  1   -0.316483  1    3   2   7
H    1.098206  1  122.715210  1 -179.684021  1    3   2   7
0    0.000000  0    0.000000  0    0.000000  0    0   0   0
C     .000000  0     .000000  0     .000000  0    0   0   0
C    1.506600  1     .000000  0     .000000  0    1   0   0
C    1.418947  1  116.688263  1     .000000  0    2   1   0
H    1.118077  1  111.116249  1  -59.952415  1    1   2   3
H    1.119762  1  109.783371  1 -179.449097  1    1   2   3
H    1.118210  1  111.069687  1   61.123405  1    1   2   3
H    1.150598  1  110.672989  1  174.990601  1    2   1   4
H    1.150955  1  110.650314  1   64.874481  1    2   1   4
H    1.109621  1  121.247902  1 -179.729874  1    3   2   1
H    1.110257  1  121.556961  1     .300391  1    3   2   1
0     .000000  0     .000000  0     .000000  0    0   0   0

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

This time MOPAC produced a structure of transition state which 
is almost the same as that of reactants, that is, there was 
almost no change between reactants and transition state.

I've tried to refine the transition state with the key words,
"TS", "SIGMA", and "NLLSQ" separately, which gives no change
either.

Why is the result like this?  Could anyone PLEASE tell me how 
can I go further to obtain a reliable structure of the 
transition state??

Thank you VERY MUCH in advance.

####################(Answers)########################

From [email-masked] Jul 27 11:24:00 1996
Date: Wed, 10 Jul 1996 10:56:02 -0500
From: "Leif P. Olson" <[email-masked]>
To: [email-masked]
Subject: mopac ts

Hi Tae-Yun,

I would suggest taking a different approach altogether, breaking
up the problem into several parts:

1) get an approximate transition state for the reaction.  Forget
about SADDLE and so forth; just do a trajectory calculation where
you start with your 1-n-propyl cation and stretch the bond in
small increments (say, 0.1 angstroms) from the starting point to
about 4 or 5 angstroms.  Remember, by microscopic reversibility,
the ts for the reverse reaction is precisely the same as the 
forward reaction.  Also, by starting with one molecule rather 
than two, you can be pretty sure that the program will not get
confused about how to assign the electrons in the orbitals, at 
least in the early stages of the reaction.

2) take the highest point in the trajectory and see if it seems
like some reasonable structure.  If so, change the coordinate 
system from internal coordinates (used in the trajectory calculation)
to xyz coordinates.  Searches using the TS keyword, in my experience,
almost always benefit from being done in Cartesian coordinates
(despite what the manual says regarding the use of this in only
difficult cases).  The eigenvector-following algorithm works
pretty well (TS keyword).  

3) Once you have a refined TS structure, you may want to refine
it a bit further; i.e., if you are quite close to a symmetric 
structure, you may want to go back to internal coordinates and
make 179.8 degree dihedrals to 180.000, for example.  This 
must be done judiciously, but can in some cases overcome rounding
errors that creep in.  Now try another TS calculation (or NLLSQ
or SIGMA) using tighter optimization criteria.

4) Do a FORCE calculation to see if you are at a true transition
state

5) Do an IRC run to make sure that the transition state you have
actually goes to reactants and products (actually this requires
two IRC runs).

If you used the PRECISE keyword in step 2, you can generally 
skip step 3 entirely.  But the general pattern has proven 
successful for me in the past.  The two most important points
seem to be (i) having a good guess at an approximate transition
state; and (ii) using the combination of XYZ and TS.

As a separate issue: why not do good-quality ab initio calculations
instead?  You only have three heavy atoms.

Leif Olson		[email-masked]

From [email-masked] Jul 27 11:24:06 1996
Date: Wed, 10 Jul 1996 11:47:12 -0500
From: Irene Newhouse <[email-masked]>
To: [email-masked]
Subject: Re: CCL:M:Searching transition state with MOPAC; part2

Try your latest structure in a frequency computation & see if there is indeed
1 & only 1 'negative' frequency [it's really imaginary, but is reported as
negative by the program].  I've found transition states to be very nonintuitive.
Not surprising, since so little experimental work can be done!  The 'obvious'
choices for TSs, I've found, are often  plain wrong!!!  If this is not indeed
a very reactant-like TS, & you still haven't located it, look at the literature
& see if you can find a similar computation somewhere.  Use that as a model,
no matter how strange it looks, & see where it gets you.  

For example, see Foresman & Frisch's book on using Gaussian for the Formal-
dehyde decomp/formation rxn from CO & H2.  I'd not have guessed that TS struc-
ture in a month of Sundays, yet that's what it is!

Good luck!
Irene Newhouse

From [email-masked] Jul 27 11:24:11 1996
Date: Wed, 10 Jul 1996 12:49:16 -0400 (EDT)
From: Stanislaw Oldziej <[email-masked]>
To: [email-masked]
Subject: Transition state

Hi

1. In my opinion you substrates and product are to "far" one to each 
anothera. Try to optimize substrate compex and products. You should 
expect that substrates are formed pi-complex stabilized by interaction 
between empty p-orbital of the carbocation and pi-orbitals of ethylene. I 
thing that distans carbon-carbon should be in range 3-2.2 A but not 8 
(see your input). If you have optimized complexes than run SADDLE.

2. If you not find TS using procedure from point 1. Try PATH option with 
changing distance between two atoms your input schould look like:

CHARGE=1 PRECISE
Me--->p methylation activated complex
 
C     .000000  0     .000000  0     .000000  0    0   0   0
C    1.500000 -1     .000000  0     .000000  0    1   0   0
C    1.418947  1  116.688263  1     .000000  0    2   1   0
H    1.118077  1  111.116249  1  -59.952415  1    1   2   3
H    1.119762  1  109.783371  1 -179.449097  1    1   2   3
H    1.118210  1  111.069687  1   61.123405  1    1   2   3
H    1.150598  1  110.672989  1  174.990601  1    2   1   4
H    1.150955  1  110.650314  1   64.874481  1    2   1   4
H    1.109621  1  121.247902  1 -179.729874  1    3   2   1
H    1.110257  1  121.556961  1     .300391  1    3   2   1
0     .000000  0     .000000  0     .000000  0    0   0   0
2.0 3.0 4.0 5.0 6.0 7.0 8.0

You can start from product to substrates (like in example) or in reversed 
direction. After this you should select structure with the highest energy 
and try to optimized it by NLLSQ and/or TS.

3. You should done calculation using another methods AM1, PM3

Stanislaw Oldziej

P.S. Sorry for my still bad English

From [email-masked] Jul 27 11:24:16 1996
Date: Wed, 10 Jul 96 12:29 CDT
From: "George P. Ford" <[email-masked]>
To: [email-masked]
Subject: Re: CCL:M:Searching transition state with MOPAC; part2

Dear Pack:

I have a couple of comments on your study that might be useful. One refers 
specifically to the transition state problem, the other relates to the 
philosophy of your study.

The use of saddle is best reserved for complex situations were several bonds are
being made and broken at the same time. Reactions like yours, where the 
transition vector can be anticipated to involve essentially the formation of a 
single bond, are almost always best studied by following a simple reaction 
coordinate for the reverse reaction. (This might be a bit less clear-cut if you 
were not using a Z-matrix-based geometry definition). This also has the 
advantage of immediately identifying those reactions where there is no 
transition state per se, i.e. the energy simply falls monotonically from 
reactants to products.

A quick look at your system at the AM1 level shows it to be a reaction of this 
kind. There is no t.s. - the energy rises to a plateau corresponding to the 
dissociation energy. A saddle calculation should end up at some arbitrary point 
on that plateau which it apparently did.

While this exercise has hopefully illustrated something about locating 
transition states it probably isnUt the way to study the chemistry of carbenium 
ions. The trouble is that the potential surfaces given by AM1, and MNDO (I 
assume also PM3) are completely wrong. The relative ordering, and even the 
nature (minimum vs t.s.) of most of the stationary points is incorrect. For 
example, corner protonated cyclopropane which is probably an intermediate on the
true reaction path you are seeking is incorreclty predicted by these methods to 
be a saddle point. Conversely, the primary propyl cation, predicted to be a 
minimum at the semiempirical level, is actually a saddle point.

Hope this helps,

George P. Ford

============================================================================
George P. Ford                      |     email:  [email-masked]
Department of Chemistry             |       web:  http://www.smu.edu/~gford/
Southern Methodist University       | telephone:  (214)768-2479
Dallas, Texas 75275                 |       fax:  (214)768-4089
============================================================================

From [email-masked] Jul 27 11:24:24 1996
Date: Wed, 10 Jul 1996 13:11:17 -0700 (PDT)
From: Kimberley Cousins <[email-masked]>
To: [email-masked]
Subject: TS location

Hi.  I've had limited luck with Saddle, and usually use the "reaction 
coordinate" approach.  Your first Z matrix is set up to do just that.  
Instead of "1" for C1-C2 bond length opt, use "-1" and list a series of 
decreasing bond lenghths following a blank line following the Z matrices 
(like 7.1, 6.1, 5.1 . . .) and look for the highest energy structure 
generated that doesn't otherwise fly apart.  This should (might) be your 
approx TS structure that you can optimize further using NLLSQ or the like.

Kimberley Cousins
Department of Chemistry
California State University, San Bernardino
5500 University Parkway
San Bernardino, CA  92407

(909)880-5391
[email-masked]

From [email-masked] Jul 27 11:24:34 1996
Date: Fri, 12 Jul 1996 17:12:21 +0100 (NFT)
From: Van Keer Annik <[email-masked]>
To: "Park, Tae-Yun" <[email-masked]>
Subject: transition state

Hello Park,

I donnot know if I can help you with your Mopac version because I am
a Gaussian user.  Firstly I do not understand why the bond between C1 and 
C2 is so large: 8.47 A? If you take 3 A or 3.5 A as distance between these 
bonds than you also have two reactants without any interaction. I guess 
that any change in geometry than  will earlier lead to a transition state 
for which I guess that the initially formed CC bond is about 1.8 A. 
Secondly, I do not know which optimization procedure you are using, but 
as I see two inputs one for the reactants and another one for the products I 
guess 
your program is looking for a TS via a LST path. In this case you have to 
identify two identically z-matrices, with of course different parameters, 
which you didn't.
 Thirdly, it is possible that the addition of CH3(+) to C2H4 is a barrier 
free proces. I know that the addition of triplet CH2 to C2H4 is barrierfree.
I hope that you can use my suggestions.

Good luck,

Annik

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

 Annik Van Keer 
 Katholieke Universiteit Leuven
 Laboratorium voor Quantumchemie
 Celestijnenlaan 200F
 3001 Heverlee, Belgium

 Tel:00-32-16-327384
 Fax:00-32-16-327992
 E-mail:[email-masked]