Subject: Help!: How to visualize the (+)-charged carbon atom?

From: "Park, Tae-Yun" <[email-masked]>
Date: Sat, 3 Aug 1996 16:08:30 +0200 (DFT)

Dear all,

This message is to ask some help how I can visualize/describe 
the positively-charaged carbon atom in a transition molecule by 
using molecular/electronic density plot with a suitable graphical 
software.

Please execuse me if this message is concerning too basic 
or not suitable for people in the field of comutational chemistry,
as I'm not a quantum chemist although I need some knowledge in 
this field for my Ph.D. work.

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My question is the following:
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I'm using MOPAC93 for various semiempirical calculations and
Molden/Chem 3D Pro to visualize the results obtained from
MOPAC93.  I'm mainly interested in the description of a molecule
contains (+)-charged carbon atom. 

Please consider the following simple situation.

To get the optimized geometry and heat of formation of secondary
propyl carbenium ion,C-C(+)-C, I executed the the MOPAC93 with
the keywords, "CHARGE=1 AM1 GEO-OK EF PRECISE DENSITY GRAPH".

With this running of MOPAC93, I've got several result files,
such as "*.arc, *.den, *.gpt, and  *.out".  The optimized geometry
and final heat of formaiton is available in the file "*.out"

If I edit the final/optimized geometry using molden/Chem3D Pro, 
however, all I can see is the 3-dimensional molecule structure 
of the optimized secondary propyl carbenium ion, and there is 
no information of the (+)-charged carbon atom in this figure;
if someone who doesn't know chemistry well look at this 3D 
structure, he never knows which carbon atom is (+)-charged.

In order to visualize the characteristic of the (+)-charged 
carbon atom, I believe I have to draw molecular/density plot
for the secondary propyl carbenium ion, right??  

My problem is starting from here.  The molden software is the 
only thing I have which is able to draw some molecular density.  
By input one of the result files, "*.gpt" into molden, I can draw 
various molecular density plots, such as HOMO(Highest Occupied 
Molecular Orbitals), LUMO(Lowest Unoccupied Molecular Orbitals), 
Norm. Density, Bond, Orbitals, etc... More exactly there are about 
23 different plots availabe in molden. (19 Orbitals + HOMO +
LUMO + Norm. Density + Bond).

But what are these?  Which one is suitable for visualizing
the (+)-charged carbon atom and why??  Am I standing in the 
correct way? Or is there any other methods/softwares to this??

The manual of molden software gave me almost no help, very 
probably due to my lack of knowledge of quantum chemistry.
Is it possible to characterize the (+)-charged carbon 
atom with mopac output and some graphical software??

Of course, my question written above is not the final goal I want 
to reach. The reason of the question will be explained below. 

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The reason of my question is the following:
==================================================================

Thanks to the great help from the members of CCL, I was able to
find out the structure of the transition state in the reaction,

                    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
   ion                                      ion

The transition state(TS) was edited by molden/Chem3D Pro and shows 
that (i) the double bond in the propene still exist, and (ii) the TS 
is more close to reactants.

But I want to know more about this transition state as followins.
 
  1. Does the double bond in the TS has the same strength as in the 
     reactant(propene)? Isn't it partially broken?  If so, how 
     can I visulaize/describe this partially broken double bond??

  2. What about the (+)-charged carbon atom in TS? Is it also almost
     no difference from the (+)-charged carbom atom of the reactant
     carbenium ion(secondary propyl carbenium ion)??

  3. What about the new bond formed between two reactants in TS?
     Isn't it partially formed?  If so, again, how can I 
     visulaize/describe this partially formed bond??

All these questions are not possibly answered by just editing the 
 TS in 3-dimensional molecular structure.  But is it possible
to get some answers of these questions by using molecular/electronic
density plots?  

It would be GREATLY APPRECIATED if you could let me know ANY
information/advice on my questions written above. I also attached 
my TS structure in MOPAC fomat 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]
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

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TS structure(refined by NLLSQ):
----------------------------------------------------------------

 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

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