From owner-chemistry@ccl.net Tue Dec 28 13:45:00 2010 From: "Loan Huynh huynhkl2000**yahoo.ca" To: CCL Subject: CCL: calculation of logP using atom contribution Message-Id: <-43463-101228104727-18940-PDFeIg+A/R0l5puyy2AnmA]*[server.ccl.net> X-Original-From: Loan Huynh Content-Type: multipart/alternative; boundary="0-1766933784-1293551236=:38340" Date: Tue, 28 Dec 2010 07:47:16 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000#yahoo.ca] --0-1766933784-1293551236=:38340 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi Stephen, Thank you very much for your answer. According to Grosh and Crippen model, = I need=0A"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= =0Aoxidation state with the data report in scheme 1 of Mannhold paper (J. C= omputer-Aided=0AMolecular Design, 2001, 15, 337). =0A=0A=C2=A0=0A=0AFor exa= mple, quinidine has one methylene group with 2H.=0AAccording to your calcul= ation, the oxidation state of this group is -2 (by the=0Away, methylenes ha= ve carbons of sp2, not sp3). I checked scheme 1 of Mannhold=0Apaper to see = if the author report any 2H attached to carbon of sp2 with oxidation=0Astat= e of 2. However, Mannhold reported only 1 H with carbon type sp3 with=0Aoxi= dation state 2.=20 Is there a different way for calculate the formal oxidation? thank you very= much for your help. Loan =0A=0A --- On Fri, 12/24/10, Stephen Bowlus chezbowlus#,#comcast.net wrote: "Formal charge" and "oxidation state" are different animals. =C2=A0The oxid= ation state of nitrogen in an ammonium ion is -3; its formal charge is +1. I don't see=0A how it is possible for a=0A carbon bearing only 1 hydrogen (= all other connections to carbon) to have an oxidation number =3D 0; but it = is very likely that the carbon would have formal charge =3D 0.=C2=A0In quin= idine, all the carbons have a formal charge of 0. =C2=A0But their oxidation= =0A states vary: for example: -2 (sp3 C in methyl group in methoxy =C2=A0- = -3 to balance 3 H and +1 to balance 1/2 an oxygen); +1 (aromatic "sp2" C wi= th methoxy substituent); 0 (!, sp3 bridge bearing hydroxyl group - 0 for ca= rbon 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? =C2=A0It'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,=C2=A0 Thank you very much for your help. As you suggest, I did try to calculate t= he oxidation number base on general rule (http://en.wikipedia.org/wiki/Oxid= ation_state). =C2=A0 However, when I apply general rule for calculating formal charge of carbon,= I can=E2=80=99t get the formal charge reported in Grosh and Crippen ( J. C= omputational Chemistry, 1988, 9, p.80-90) paper.=C2=A0 According to Mannhold (J. Computer-Aided Molecular Design, 2001, 15, 337),= =0A Quinidine has 1 H that attached to Csp3 with formal charge of 0. It see= m like=0A the general rule is not applicable to this case. =C2=A0=C2=A0 Then I try another method for calculating formal oxidation number. Accordin= g to Viswanadhan (J. Chem. Inf Comput. Sci. 1989, 29, 163), =E2=80=9Cthe fo= rmal oxidation number of a carbon atom =3D sum of formal bond orders with e= lectronegative atoms=E2=80=9D, so H that attached to Csp3 with carbon has f= ormal charge of 3. However, Mannhold didn't report any functional group tha= t have 1H attached to Csp3 with carbon has formal charge of 3.=20 =C2=A0 Any other suggestion is greatly appreciate. =C2=A0 Loan =C2=A0 --- On Wed, 12/22/10, Stephen Bowlus chezbowlus.:.comcast.net =0A wrote: 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=0A depending on how=0A the carbon=0A is subst= ituted, but the _change_ in oxidation states in the course of reaction seem= s 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 relevan= t; otherwise, oxidation state is calculated on a completely non-physical ba= sis. 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=20 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=0A 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 --0-1766933784-1293551236=:38340 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hi Stephen,

Thank you very much for yo= ur answer. According to Grosh and Crippen model, I need=0A"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 o= f the=0Aoxidation state with the data report in scheme 1 of Mannhold paper = (J. Computer-Aided=0AMolecular Design, 2001, 15, 337). =0A=0A

 

=0A=0A

For example, quinid= ine has one methylene group with 2H.=0AAccording to your calculation, the o= xidation state of this group is -2 (by the=0Away, methylenes have carbons o= f sp2, not sp3). I checked scheme 1 of Mannhold=0Apaper to see if the autho= r report any 2H attached to carbon of sp2 with oxidation=0Astate of 2. Howe= ver, Mannhold reported only 1 H with carbon type sp3 with=0Aoxidation state= 2.


=

Is there a d= ifferent way for calculate the formal oxidation? thank you very much for yo= ur help.


=

Loan

= =0A=0A

--- On Fri, 12/24/10, Stephen Bowlus c= hezbowlus#,#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.
<= br>
I don't see=0A how it is possible for a=0A carbon bearing onl= y 1 hydrogen (all other connections to carbon) to have an oxidation number = =3D 0; but it is very likely that the carbon would have formal charge =3D 0= . In quinidine, all the carbons have a formal charge of 0.  But t= heir oxidation=0A states vary: for example: -2 (sp3 C in methyl group in me= thoxy  - -3 to balance 3 H and +1 to balance 1/2 an oxygen); +1 (aroma= tic "sp2" C with methoxy substituent); 0 (!, sp3 bridge bearing hydroxyl gr= oup - 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 ri= ngs).

So do you need oxidation states or formal ch= arges?  It's been too long for me to remember any details of the Ghosh= and Crippen model.

-sb

<= div>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 r= ule (http://en.wikipedia.org/wiki/Oxidation_state).

 

However, when I apply general rule for calcula= ting formal charge of carbon, I can=E2=80=99t get the formal charge reporte= d in Grosh and Crippen ( J. Computational Chemistry, 1988, 9, p.80-90) pape= r.

 

Accor= ding to Mannhold (J. Computer-Aided Molecular Design, 2001, 15, 337),=0A Qu= inidine has 1 H that attached to Csp3 with formal charge of 0. It seem like= =0A the general rule is not applicable to this case.  = ;

 

Then I try another method for calcul= ating formal oxidation number. According to Viswanadhan (J. Chem. Inf Compu= t. Sci. 1989, 29, 163), =E2=80=9Cthe formal oxidation number of a carbon at= om =3D sum of formal bond orders with electronegative atoms=E2=80=9D, 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 carb= on has formal charge of 3.

 

Any other s= uggestion is greatly appreciate.

 

Loan

 
--- On Wed, 12/22/1= 0, Stephen Bowlus chezbowlus.:.comcast.net <owner-chemistry^ccl.net&g= t;=0A wrote:
What seems to work is the = usual rules, supplemented by the rule: bonds to the same element don't coun= t. 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 o= xygen =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 jus= tified on the basis that the electrons in a bond between the same elements = are shared equally.

One does get some wierdnesses=0A depe= nding on how=0A the carbon=0A is substituted, but the _change_ in oxidation= states in the course of reaction seems reasonable. So the concept is succe= ssful as a bookkeeping method. One has to remember that it is the change in= most cases that is physically relevant; otherwise, oxidation state is calc= ulated on a completely non-physical basis.

There i= s actually a nice Wikipedia article "Oxidation State" that shows situations= as carbon's oxidation state varies from +4 (carbon tetrachloride) to -4 (m= ethane).  For an acetylene that you describe, I would calculate the ox= idation 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 P= M, Loan Huynh

Dear CCL,

I am currently calculating th= e logP values using the atom contribution by Grosh and Crippen ( J. Computa= tional Chemistry, 1988, 9, p.80-90).

 
I have done quite a lot of searching on calculating the ox= idation state of carbon. However, I have trouble calculating the formal oxi= dation number of various hybridization carbons.  For example, for H attached to sp carbon, I cannot obtain the formal cha= rge of 3 for sp carbon. 

 

Is there any document that=0A shows th= e calculation of oxidation number for sp carbon? 

 

Thank you very m= uch for your help,

 

Lo= an







<= /td>


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