Subject: CCL:2 unrelated questions

From: "George P. Ford" <[email-masked]>
Date: Wed, 28 May 97 12:08 CDT

Dr. S. Shapiro writes:
> 
> 
> Dear Colleagues;
> 
>         I have two quite unrelated questions for which perhaps some CCLers
> might be able to provide useful replies:
> 
> Question 1:  In order to obtain Mulliken partial atomic charges for some
> work in which we are engaged, I prepared a Z-matrix for the molecule
> p-tolylacetylene ("tolac.mop"), as follows:
> 
> 
> am1 nointer
> p-tolylacetylene
> 
> C     0.000000  0    0.000000  0    0.000000  0   0   0   0 
> C     1.401729  0    0.000000  0    0.000000  0   1   0   0 
> C     1.399999  0  120.081459  0    0.000000  0   2   1   0 
> C     1.399809  0  120.056900  0    0.000000  0   3   2   1 
> C     1.399806  0  119.942001  0    0.000000  0   4   3   2 
> C     1.400006  0  120.056679  0    0.000000  0   5   4   3 
> C     1.312333  0  120.109207  0  180.000000  0   1   2   3 
> C     1.200200  0  179.891647  0  180.000000  0   7   1   2 
> H     1.103619  0  119.699532  0  180.000000  0   2   3   1 
> H     1.103127  0  119.972672  0  180.000000  0   3   2   1 
> H     1.103111  0  120.028992  0  180.000000  0   4   3   2 
> H     1.103127  0  119.970596  0  180.000000  0   5   4   3 
> H     1.103619  0  119.699341  0  180.000000  0   6   5   4 
> H     1.059943  0  180.000000  0  180.000000  0   8   7   1 
> 
> 
The problem is that the dihedral angle for the acetylenic hydrogen is 
ill-defined because the defining atoms (8, 7, 1) are linear. The standard 
solutionis to add a dummy atom. For example, you could replace the last line of 
your Z-matrix by:

XX     1.0       0   90.0       0    0.0       0   8   7   6
 H     1.059943  0   90.000000  0  180.000000  0   8   9   7

This adds a dummy (XX) which redefines H14 in terms of three non-linear atoms:
       
                 X9     C6-C5
                 |     /    \
             H14-C8-C7-C1    C4
                       \    /
                        C2-C3

An alternative approach would be to use a Cartesian definition (include the 
keyword XYZ). This of course depends on your either having a compelete set of 
xyz coords available or being willing to figure out the missing set (for H14) 
and add them manually.
> 
> 
> Question 2:  I would like to know if there is some established quantitative
> measure of the "degree" of chirality.  For example, consider the chiral
> molecules CR1R2R3R4, where in one case R1 = H, R2 = D, R3 = T, and R4 = F,
> whereas in another case R1 = H, R2 = naphthyl, R3 = n-octyl, and R4 = NO2.
> Whilst both molecules are chiral, it is clear that the structural variation
> when R1 = H, R2 = naphthyl, R3 = n-octyl, and R4 = NO2 makes this a "more"
> chiral molecule than when R1 = H, R2 = D, R3 = T, and R4 = F.  But how to
> express in a quantitative fashion that the second chiral molecule is "more"
> chiral than the first?  I thought that perhaps the RMS deviation between the
> two enantiomorphs of each of these chiral molecules might provide
> quantification of chirality.  Does anyone have any further, possibly better,
> suggestions?
> 
By definition a molecule is either chiral or it isn't. Admittedly, the physical 
manifestation of chirality when the chirality is due only to isotopic 
substitution (the rotation of plane polarized light), is tiny. But this is a 
special situation. Such generalizations are rare for chemical substitutions. 

I think that to define "degree of chirality" in the way you suggest is just to 
define a degree of molecular similarity. In that sense it's not fundamentally 
different from comparing the similarity of any two molecules.

Without knowing more about your ultimate goals its hard to be specific. However,
I would incline towards some definition that was itself inherently chiral. 
Indices obtained in this way would then have a diasteriomeric character which 
might have a better chance of paralleling the chemical consequences of what you 
are refering to as "degree of chirality". 

Perhaps you could design some kind of real or artificial chiral "probe group" 
for investigating the surface of one of the enantiomers, or perhaps some kind of
chiral envelope or cavity onto which to fit it. A different approach, for 
molecules with chiral centers, might be to try to quantify the R/S definition. 
Instead of using the sequence rules perhaps you could use some kind of 
electronic and/or size criterion. Again, this rather depends on your ultimate 
purpose.

Hope some of this is useful.

George P. Ford

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