Miguel wrote:
In the course of working on this I observed something that is going to
raise questions in the future:
*****
THE AUTOBONDING RULES STATE THAT TWO ATOMS WITH NON-ZERO CHARGES THAT HAVE
THE SAME SIGN CANNOT BOND, EVEN IF THEY ARE WITHIN NORMAL BONDING RANGE.
*****
This seems to make sense to me, given my naive understanding of charges.
Q: Does this rule make sense?
Are these "formal charges" or "partial charges"? (I assume FORMAL.)
FORMAL charges depend explicitly on how the bonding is defined. So,
technically, if you know the formal charge on an atom, you MIGHT be
able to figure out the bonding. For example, H2SO4:
HO-SO2-OH
Is that central unit O=S=O or (1-)O-S(2+)-O(1-)?
People disagree.
But the PARTIAL charge is defined without regard to bonding.
So it only makes sense to be using FORMAL charge here in terms of
determining bonding connections.
Another example:
carbon monoxide. Is that (1-)C-(triple bond)-O(1+) or C=O, no charges?
Your choice. It's just formal charge.
I fear that this is going to raise questions because someone is going to
put two positively charged carbons next to each other in an .xyz file for
.pdb file and expect them to bond.
Q: Are there legitimate cases where two positively/negatively charged
atoms can bond?
FORMALLY, probably not. PARTIALLY, sure. That's ubiquitous. Here's a
quick calculation for CH3(+):
NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS
ATOM NO. TYPE CHARGE No. of ELECS. s-Pop
1 C 0.654881 3.3451 1.35158
2 H 0.115047 0.8850 0.88495
3 H 0.115029 0.8850 0.88497
4 H 0.115043 0.8850 0.88496
clearly all the bonded atoms are partially positive. FORMALLY, though,
we just assign the charge to C and call it (1+).
It would be possible for me to remove this restriction, but I fear that it
may cause ionic bonding in areas where it does not make sense.
I can think of an esoteric case or two where one might have lots of
negative charge spread around a molecule. (H2BN comes to mind.) But if
someone has such an esoteric structure, they can't espect perfection.
Still, it seems to me that the bond distance, not the formal charge,
would define at least the SINGLE bond in this case. Maybe a compromise
would be to not add second or third bonds if the formal charges are
crazy.
But, maybe I don't understand. If the formal charges are known, this
SHOULD absolutely define exactly the bonding.....
So, for example, in allyl anion, [CH2CHCH2](1-), you won't know where
to the draw the double bond until I tell you where the formal charge
is. And if I DO tell you where the formal charge is, you should be
able to figure out for yourself where the double bond is. But no
matter what I say, there should be a SINGLE bond between adjacent
carbons just based on bond distance.
Bob Hanson
Miguel
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
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