Hi Stephen,
Thank you very much for your answer.
According to Grosh and Crippen model, I need
"formal oxidation number". I assume that "formal oxidation number" is the
oxidation state.
I follow your calculation but still I can not match the
calculation of the
oxidation state with the data report in scheme 1 of Mannhold paper (J.
Computer-Aided
Molecular Design, 2001, 15, 337).
For example, quinidine
has one methylene group with 2H.
According to your calculation, the oxidation state of this group is -2 (by the
way, methylenes have carbons of sp2, not sp3). I checked scheme 1 of Mannhold
paper to see if the author report any 2H attached to carbon of sp2 with
oxidation
state of 2. However, Mannhold reported only 1 H with carbon type sp3 with
oxidation state 2.
Is there a different way
for calculate the formal oxidation? thank you very much for your help.
Loan
--- On Fri, 12/24/10, Stephen Bowlus
chezbowlus#,#comcast.net
<owner-chemistry^-^ccl.net> wrote:
"Formal charge" and "oxidation state" are different animals. The
oxidation state of nitrogen in an ammonium ion is -3; its formal charge is
+1.
I
don't see
how it is possible for a
carbon bearing only 1 hydrogen (all other connections to carbon) to have an
oxidation number = 0; but it is very likely that the carbon would have formal
charge = 0. In quinidine, all the carbons have a formal charge of 0.
But their oxidation
states vary: for example: -2 (sp3 C in methyl group in methoxy - -3 to
balance 3 H and +1 to balance 1/2 an oxygen); +1 (aromatic "sp2" C with methoxy
substituent); 0 (!, sp3 bridge bearing hydroxyl group - 0 for carbon links, -1
to balance H and +1 to balance 1/2 O); and -1 (aromatic "sp2" C bearing
hydrogens); -2 (sp3 methylenes in quinuclidine
rings).
So do you need oxidation states or formal
charges? It's been too long for me to remember any details of the Ghosh
and Crippen model.
-sb
On
Dec 23, 2010, at 9:07 AM, Loan Huynh huynhkl2000 : yahoo.ca wrote: Hi
Steve,
Thank you
very much for your help. As you suggest, I did try to calculate the oxidation
number base on general rule (http://en.wikipedia.org/wiki/Oxidation_state).
However, when
I apply general rule for calculating formal charge of carbon, I canât get
the formal charge reported in Grosh and Crippen ( J. Computational Chemistry,
1988, 9, p.80-90) paper.
According to
Mannhold (J. Computer-Aided Molecular Design, 2001, 15, 337),
Quinidine has 1 H that attached to Csp3 with formal charge of 0. It seem like
the general rule is not applicable to this case.
Then I try
another method for calculating formal oxidation number. According to Viswanadhan
(J. Chem. Inf Comput. Sci. 1989, 29, 163), âthe formal oxidation number of
a carbon atom = sum of formal bond orders with electronegative atomsâ, so H
that attached to Csp3 with carbon has formal charge of 3. However, Mannhold
didn't report any functional group that have 1H attached to Csp3 with carbon has
formal charge of 3.
Any other
suggestion is greatly appreciate.
Loan
--- On Wed, 12/22/10, Stephen Bowlus chezbowlus.:.comcast.net
<owner-chemistry^ccl.net>
wrote:
What seems to work is the usual rules,
supplemented by the rule: bonds to the same element don't count. In the usual
formulation of the rules, this addition is a generalization of "elements have an
oxidation state of 0" and is why the "exception" of oxygen = -1 in peroxides
works. The only place this is addressed, as far as I know, is in general
chemistry texts. The expanded rule can be justified on the basis that the
electrons in a bond between the same elements are shared equally.
One
does get some wierdnesses
depending on how
the carbon
is substituted, but the _change_ in oxidation states in the course of reaction
seems reasonable. So the concept is successful as a bookkeeping method. One has
to remember that it is the change in most cases that is physically relevant;
otherwise, oxidation state is calculated on a completely non-physical
basis.
There is actually a nice Wikipedia article
"Oxidation State" that shows situations as carbon's oxidation state varies from
+4 (carbon tetrachloride) to -4 (methane). For an acetylene that you
describe, I would calculate the oxidation state as -1. C-1 of propyne
would be -1, C-2 would be 0 and C-3 would be -3. The four H's (a +1 each) make
the molecule neutral.
Steve On
Dec 22, 2010, at 12:31 PM, Loan Huynh
Dear
CCL,
I am currently calculating the logP values using the atom
contribution by Grosh and Crippen ( J. Computational Chemistry, 1988, 9,
p.80-90).
I
have done quite a lot of searching on calculating the oxidation state of carbon.
However, I have trouble calculating the formal oxidation number of various
hybridization carbons. For example, for H attached
to sp carbon, I cannot obtain the formal charge of 3 for sp carbon.
Is
there any document that
shows the calculation of oxidation number for sp carbon?
Thank
you very much for your help,
Loan
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