Subject: Help!: IRC by mopac

From: "Park, Tae-Yun" <[email-masked]>
Date: Wed, 17 Jul 1996 15:28:33 +0200 (DFT)

Dear all,

*************************************************************
I'm sending this message one more time, since my previous
e-mail was not responded in more than 1 day.  Please execuse
me if you receive this message twice.
*************************************************************

I'm searching the structure of the transition state with 
mopac for the reaction type,

    olefin + carbenium ion ---> (TS?) ---> carbenium ion  (1)

My previous try for 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

has been found that there is no transition state, thanks to 
great help from many CCLers, since the gas-phase methyl 
carbenium ion is too unstable.

Actually I'm dealing with more than 100 reactions which have
the reaction type written in (1).  Therefore, I tried with 
other reaction, which contains more stable species, i.e.,

                    H  
                    |                      H
    H         H   H-C-H                   HCH H H H
  H | H        \   /                     H |  | | |  
 HC-C-CH   +    C=C    ---->(TS?)---->  HC-C--C-C-C-H
  H + H        /   \                     H |  | + |
              H     H                      H  H   H
secondary
  propyl      propene                   secondary 2-M
carbenium                              pentyle carbenium

Searching the TS in this reaction, I followed the suggestion
by many CCLers, i.e., try to get the TS structure by the 
following steps instead of using SADDLE calculation:

1. Try the reacion path calculation in mopac and save the 
   structure that contains the highest energy level.

2. Refine the structure at highest energy level with key 
   word, NLLSQ, or SIGMA, or TS.

3. FORCE calculation with the refined structure to check 
   if there is one and only one negative frequecy value.

4. Do IRC(=1 and -1) calculation to check if the refined 
   TS gives the reactants and product.

My result is that until step 3, everything seems OK.  Refinning
the TS by NLLSQ/SIGMA/TS gives no significant change of the TS
that obtained from step 1, probably because I used the key word
PRECISE in step 1.  The FORCE calculation showed that the refined
structure contains only one frequency values.

My problem is in the last step.  When I do the IRC calculation
and try to look at the result structure with "molden" software,
it gives exactly same as the structure of TS I input.

I wonder if (i) my TS is not correct, or (ii) the IRC calculation
doesn't give the molecular structure result from the calculation
so that molden only edit the structure I input.  In the latter
case, however, I don't know how to edit the molecluar structure
generated by IRC calculation.

Could anyone PLEASE help me how to confirm my TS structure by IRC?

I enclosed the input/result file at the end of this message.

Thank you very much in advance.

				Sincerely,

				     Park, TAE-YUN    
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
State University of Ghent
Laboratorium voor Petrochemische Techniek
Krijgslaan 281, Blok S5  
9000 Gent, Belgium	  
TEL:+(32)-0(9)-264-4527
FAX:+(32)-0(9)-264-4999
e-mail: [email-masked]
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Data Files for the 4 steps.  Please note that the result file of 
step 1 is the input file for step 2... etc.

----------------------------------------------------------------
Step 1 input file:

CHARGE=1 PRECISE GRAPH DENSITY
r3_s-o3.dat

C    0.000000  0    0.000000  0    0.000000  0    0   0   0
C    1.437805  1    0.000000  0    0.000000  0    1   0   0
C    4.501968 -1   96.018692  1    0.000000  0    1   2   0
C    1.331116  1   87.080215  1 -155.227356  1    3   1   2
C    1.476334  1  124.262665  1 -135.173477  1    4   3   1
C    1.437424  1  123.306213  1  133.821869  1    1   2   3
H    1.135651  1  110.106583  1  123.092896  1    2   1   6
H    1.120895  1  114.528610  1    0.000000  1    2   1   6
H    1.135742  1  110.066360  1 -123.042191  1    2   1   6
H    1.115219  1  118.018661  1  -56.365555  1    1   2   7
H    1.097427  1  122.281586  1 -179.999634  1    3   4   5
H    1.097809  1  122.792145  1    0.000000  1    3   4   5
H    1.103470  1  120.865265  1    0.000000  1    4   3  11
H    1.118958  1  110.075104  1 -120.477097  1    5   4   3
H    1.119080  1  110.076859  1  120.510315  1    5   4   3
H    1.117584  1  111.867340  1    0.000000  1    5   4   3
H    1.121948  1  113.719040  1 -179.999634  1    6   1   2
H    1.134903  1  110.648621  1   57.360474  1    6   1   2
H    1.134933  1  110.636383  1  -57.367462  1    6   1   2
0    0.000000  0    0.000000  0    0.000000  0    0   0   0
4.0 3.5 3.0 2.8 2.6 2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.55

----------------------------------------------------------------
Step 2 input file(for NLLSQ):

NLLSQ CHARGE=1 PRECISE DENSITY GRAPH
Optimizing ts

 C     .000000 0     .000000 0     .000000 0       0    0    0
 C    1.493971 1     .000000 0     .000000 0       1    0    0
 C    2.400000 1   99.829562 1     .000000 0       1    2    0
 C    1.366739 1  107.774987 1 -156.603212 1       3    1    2
 C    1.495494 1  127.295132 1  -95.474920 1       4    3    1
 C    1.493103 1  122.565420 1  111.465448 1       1    2    3
 H    1.108922 1  112.541937 1  169.169618 1       2    1    6
 H    1.109391 1  113.333661 1   45.130877 1       2    1    6
 H    1.118316 1  107.399773 1  -73.220364 1       2    1    6
 H    1.098555 1  116.705711 1  -32.527608 1       1    2    7
 H    1.092716 1  119.490590 1  165.857707 1       3    4    5
 H    1.091757 1  122.354434 1    9.374023 1       3    4    5
 H    1.098702 1  118.584661 1  -13.736600 1       4    3   11
 H    1.111796 1  109.120250 1 -115.208112 1       5    4    3
 H    1.110446 1  110.429073 1  126.570168 1       5    4    3
 H    1.107787 1  113.319142 1    4.958871 1       5    4    3
 H    1.108134 1  112.416348 1 -172.721816 1       6    1    2
 H    1.118042 1  107.755456 1   69.492728 1       6    1    2
 H    1.109678 1  113.288218 1  -48.800221 1       6    1    2

----------------------------------------------------------------
Step 3 input file (for NLLSQ):

FORCE CHARGE=1 DENSITY GRAPH ISOTOPE
TS checking by FORCE calculation

 C     .000000 0     .000000 0     .000000 0       0    0    0
 C    1.494700 1     .000000 0     .000000 0       1    0    0
 C    1.493679 1  122.365784 1     .000000 0       2    1    0
 C    2.380560 1  102.504395 1  110.467232 1       2    3    1
 C    1.368080 1  107.971291 1   74.388344 1       4    2    3
 C    1.495277 1  127.264130 1  -95.821228 1       5    4    2
 H    1.108898 1  112.496826 1  169.901352 1       1    2    3
 H    1.109529 1  113.296120 1   46.004711 1       1    2    3
 H    1.117890 1  107.496994 1  -72.487534 1       1    2    3
 H    1.098734 1   86.146576 1  -42.602459 1       2    4    5
 H    1.092931 1  119.365471 1  165.091675 1       4    5    6
 H    1.092000 1  122.211273 1    9.421019 1       4    5    6
 H    1.098602 1  118.611084 1   84.593826 1       5    4    2
 H    1.111888 1  109.074448 1 -114.666496 1       6    5    4
 H    1.110686 1  110.417656 1  127.198174 1       6    5    4
 H    1.107639 1  113.346970 1    5.549870 1       6    5    4
 H    1.108230 1  112.441048 1 -172.787689 1       3    2    1
 H    1.117836 1  107.759140 1   69.464531 1       3    2    1
 H    1.109580 1  113.282127 1  -48.948452 1       3    2    1

-----------------------------------------------------------------
Step 4 input file (for NLLSQ and for backward reaction, i.e, IRC=-1)
       This step is restarted immediately after the step 3.

IRC=-1 RESTART CHARGE=1 DENSITY GRAPH ISOTOPE
TS checking by IRC calculation

 C     .000000 0     .000000 0     .000000 0       0    0    0
 C    1.494700 1     .000000 0     .000000 0       1    0    0
 C    1.493679 1  122.365784 1     .000000 0       2    1    0
 C    2.380560 1  102.504395 1  110.467232 1       2    3    1
 C    1.368080 1  107.971291 1   74.388344 1       4    2    3
 C    1.495277 1  127.264130 1  -95.821228 1       5    4    2
 H    1.108898 1  112.496826 1  169.901352 1       1    2    3
 H    1.109529 1  113.296120 1   46.004711 1       1    2    3
 H    1.117890 1  107.496994 1  -72.487534 1       1    2    3
 H    1.098734 1   86.146576 1  -42.602459 1       2    4    5
 H    1.092931 1  119.365471 1  165.091675 1       4    5    6
 H    1.092000 1  122.211273 1    9.421019 1       4    5    6
 H    1.098602 1  118.611084 1   84.593826 1       5    4    2
 H    1.111888 1  109.074448 1 -114.666496 1       6    5    4
 H    1.110686 1  110.417656 1  127.198174 1       6    5    4
 H    1.107639 1  113.346970 1    5.549870 1       6    5    4
 H    1.108230 1  112.441048 1 -172.787689 1       3    2    1
 H    1.117836 1  107.759140 1   69.464531 1       3    2    1
 H    1.109580 1  113.282127 1  -48.948452 1       3    2    1

------------------------------------------------------------------