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
=

<= /div>

= --Apple-Mail-18--921523408-- From owner-chemistry@ccl.net Thu Dec 23 11:28:01 2010 From: "William F. Coleman wcoleman:wellesley.edu" To: CCL Subject: CCL: Calculation absorption spectrum using Gaussian G03 Message-Id: <-43451-101223100247-5565-hWQPKle1wTZm+Ifyzu6lMA,+,server.ccl.net> X-Original-From: "William F. Coleman" Content-Type: multipart/alternative; boundary="--=_--22071c0a.22071b22.c939150c" Date: Thu, 23 Dec 2010 10:02:36 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman_._wellesley.edu] This is a multi-part message in MIME format. ----=_--22071c0a.22071b22.c939150c Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit An isolated gold atom is actually s1(d10f14), so I would check to make sure that the highest occupied orbital is predominately s in character, and proceed from there. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 www.wellesley.edu/Chemistry/colemanw.html http://www.flicksstuff.com/photos/pictures.html new galleries 9/4/2010 Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html ----=_--22071c0a.22071b22.c939150c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>

An isolated gold atom is actually s1(d¹⁰f¹⁴), so I would check to make sure tha= t the highest occupied orbital is predominately s in character, and proceed= from there.

Cheers,

Flick

_______________

William F. Coleman

Professor of Chemistry

Wellesley College

Wellesley MA 02481

www.wellesley.edu/Chemist= ry/colemanw.html

http://www.flicksstuff.com= /photos/pictures.html new galleries 9/4/2010

Editor, JCE WebWare and JCE Featured = Molecules

http://www.jce.divched.org/JCE= DLib/WebWare/

h= ttp://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html=

----=_--22071c0a.22071b22.c939150c-- From owner-chemistry@ccl.net Thu Dec 23 15:36:00 2010 From: "Loan Huynh huynhkl2000 : yahoo.ca" To: CCL Subject: CCL: calculation of logP using atom contribution Message-Id: <-43452-101223120745-21624-SCGD2TGrDVTtUWtLMgZpKg**server.ccl.net> X-Original-From: Loan Huynh Content-Type: multipart/alternative; boundary="0-1662746814-1293124058=:8922" Date: Thu, 23 Dec 2010 09:07:38 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000%%yahoo.ca] --0-1662746814-1293124058=:8922 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable =0A=0A=0A=0AHi Steve,=0A=0A=C2=A0=0A=0AThank you very much for your help. A= s you suggest, I did try=0Ato calculate the oxidation number base on genera= l rule (http://en.wikipedia.org/wiki/Oxidation_state).=0A=0A=0A=C2=A0=0A=0A= However, when I apply general rule for calculating formal=0Acharge of carbo= n, I can=E2=80=99t get the formal charge reported in Grosh and Crippen (=0A= J. Computational Chemistry, 1988, 9, p.80-90) paper.=0A=0A=C2=A0=0A=0AAccor= ding to Mannhold (J. Computer-Aided Molecular Design, 2001,=0A15, 337), Qui= nidine has 1 H that attached to Csp3 with formal charge of 0. It=0Aseem lik= e the general rule is not applicable to this case. =C2=A0=0A=0A=C2=A0=0A=0A= Then I try another method for calculating formal oxidation number. Accordin= g to Viswanadhan (J.=0AChem. Inf Comput. Sci. 1989, 29, 163), =E2=80=9Cthe = formal oxidation number of a carbon=0Aatom =3D sum of formal bond orders wi= th electronegative atoms=E2=80=9D, so H that=0Aattached to Csp3 with carbon= has formal charge of 3. However, Mannhold didn't report any functional gro= up that have 1H attached to Csp3 with carbon has formal charge of 3.=20 =0A=0A=C2=A0=0A=0AAny other suggestion is greatly appreciate. =0A=0A=C2=A0= =0A=0ALoan =0A=0A=C2=A0=0A=0A--- On Wed, 12/22/10, Stephen Bowlus chezbowlu= s.:.comcast.net wrote: > From: Stephen Bowlus chezbowlus.:.comcast.net Subject: CCL: calculation of logP using atom contribution To: "Huynh, Loan " Received: Wednesday, December 22, 2010, 7:56 PM What seems to work is the usual rules, supplemented by the rule: bonds to t= he same element don't count. In the usual formulation of the rules, this ad= dition is a generalization of "elements have an oxidation state of 0" and i= s why the "exception" of oxygen =3D -1 in peroxides works. =C2=A0The only p= lace this is addressed, as far as I know, is in general chemistry texts. Th= e 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, b= ut the _change_ in oxidation states in the course of reaction seems reasona= ble. So the concept is successful as a bookkeeping method. One has to remem= ber that it is the change in most cases that is physically relevant; otherw= ise, oxidation state is calculated on a completely non-physical basis. There is actually a nice Wikipedia article "Oxidation State" that shows sit= uations as carbon's oxidation state varies from +4 (carbon tetrachloride) t= o -4 (methane). =C2=A0For an acetylene that you describe, I would calculate= the oxidation state as -1. =C2=A0C-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,=20 =20 I am currently calculating the logP values using the atom contribution by = Grosh and Crippen ( J. Computational Chemistry, 1988, 9, p.80-90). =C2=A0 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. =C2=A0For example, for H attached to sp carb= on, I cannot obtain the formal charge of 3 for sp carbon.=C2=A0 =C2=A0 Is there any document that shows the calculation of oxidation number for sp= carbon?=C2=A0 =C2=A0 Thank you very much for your help,=C2=A0 Loan=20 =0A=0A --0-1662746814-1293124058=:8922 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

=0A=0A=0A=0A

Hi Steve,

=0A=0A

Thank you very much for your help. As you suggest, I did tr= y=0Ato calculate the oxidation number base on general rule (http://en.wikipedia.org/wiki/Oxid= ation_state).=0A

=0A=0A

However, when I apply general rule for calculating formal= =0Acharge of carbon, I can=E2=80=99t get the formal charge reported in Gros= h and Crippen (=0AJ. Computational Chemistry, 1988, 9, p.80-90) paper.

= =0A=0A

=0A=0A

Accordi= ng to Mannhold (J. Computer-Aided Molecular Design, 2001,=0A15, 337), Quini= dine has 1 H that attached to Csp3 with formal charge of 0. It=0Aseem like = the general rule is not applicable to this case.

=0A=0A

Then I try another method for calculating formal oxidation number. Accordi= ng to Viswanadhan (J.=0AChem. Inf Comput. Sci. 1989, 29, 163), =E2=80=9Cthe= formal oxidation number of a carbon=0Aatom =3D sum of formal bond orders w= ith electronegative atoms=E2=80=9D, so H that=0Aattached to Csp3 with carbo= n has formal charge of 3. However, Mannhold didn't report any functional gr= oup that have 1H attached to Csp3 with carbon has formal charge of 3.
<= /p>=0A=0A

=0A=0A

Any = other suggestion is greatly appreciate.

=0A=0A

&n= bsp;

=0A=0A

Loan

=0A=0A

=0A=0A--- On Wed, 12/22/10, Stephen Bowlus chezbowlus.:.comcas= t.net <owner-chemistry]_[ccl.net> wrote:

From: Stephen Bowlus chezbowlus.:.comcast.net <owner-chemis= try]_[ccl.net>
Subject: CCL: calculation of logP using atom contributio= n
To: "Huynh, Loan " <huynhkl2000]_[yahoo.ca>
Received: We= dnesday, December 22, 2010, 7:56 PM

What se= ems 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 t= he "exception" of oxygen =3D -1 in peroxides works. The only place th= is is addressed, as far as I know, is in general chemistry texts. The expan= ded rule can be justified on the basis that the electrons in a bond between= the same elements are shared equally.

One does get some wierdnes= ses depending on how the carbon is substituted, but the _change_ in oxidati= on states in the course of reaction seems reasonable. So the concept is suc= cessful as a bookkeeping method. One has to remember that it is the change = in most cases that is physically relevant; otherwise, oxidation state is ca= lculated on a completely non-physical basis.

There= is actually a nice Wikipedia article "Oxidation State" that shows situatio= ns 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 c= ontribution by Grosh and Crippen ( J. Computational Chemistry, 1988, 9, p.8= 0-90).

I have done quite a lot of searching= on calculating the oxidation state of carbon. However, I have trouble calc= ulating 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 calcu= lation of oxidation number for sp carbon?

Thank you very much for your help,

Loan

=

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