Re: CCL:G: Gaussian Linux

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 = can=92t 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), =93the formal = oxidation number of a carbon atom =3D sum of formal bond orders with = electronegative atoms=94, 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:

From: Stephen Bowlus chezbowlus.:.comcast.net = <owner-chemistry^ccl.net>
Subject: CCL: calculation of logP = using atom contribution
To: "Huynh, Loan " = <huynhkl2000^yahoo.ca>
Received: Wednesday, December 22, 2010, = 7:56 PM

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 =3D -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 huynhkl2000 _ yahoo.ca wrote:

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