From owner-chemistry@ccl.net Thu Aug 4 08:20:01 2011 From: "Olasunkanmi Lukman Olawale walecomuk::yahoo.co.uk" To: CCL Subject: CCL: mopac and mozype jobs with metal Message-Id: <-45202-110804055130-4647-TKJJIFISb9WCHI4sikbp0Q-x-server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-1536361414-1312451481=:35755" Date: Thu, 4 Aug 2011 10:51:21 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk-$-yahoo.co.uk] --0-1536361414-1312451481=:35755 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Yes.=0AGoncalo's contribution should be useful for you. If a ligand=A0is la= rgely electron =0Adonating, it might=A0alter the electronic configuration= =A0of the central =0Ametal=A0(atom/ion) without=A0you knowing it.=A0It is n= ot physical! You are presuming a =0Ad5 system, but the results were d6s for= =A0Fe.=A0One or more ligand might =0Ahave=A0donated enough electron into th= e d-orbital of the Fe,=A0especially if =0Athe=A0ligands have pi-electrons.= =0AHope this helps.=0A=A0Olasunkanmi Lukman Olawale=0A_____________________= ___________=0ACurrent Address:=0ADepartment of Chemistry,=0AObafemi Awolowo= University,=0AIle-Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-52401564 Or += 234-0-80-67161091=0A________________________________=0A=0A=0A=0A=0A=0A_____= ___________________________=0AFrom: Mark Iron mark.a.iron a weizmann.ac.il = =0ATo: "Olasunkanmi, Olawale Lukman " =0ASent: Tue, 2 August, 2011 8:20:04=0ASubject: CCL: mop= ac and mozype jobs with metal=0A=0A=0ASent to CCL by: Mark Iron [mark.a.iro= n{}weizmann.ac.il]=0AGon=E7alo=0A=0AI guess that you decided the the Fe as = determined by MOZYME to be Fe(II) based =0Ain the partial atomic charge. Re= member, that the definition of Fe(III)/Fe(II) in =0Aan enzyme (or any other= metal-organic system) is a formality based on the =0Aligands bound to it. = With the type of ligands prevalent in enzymes, it is not =0Aunexpected to f= ind partial atomic charges significantly less than the formal =0Ametal oxid= ation state. Remember that atomic charge and formal oxidation state =0Aare = not physical observables but rather tools/aids we use to help us understand= =0Athe observed chemistry.=A0 In your case, the formal +3 charge on Fe wil= l be =0Areduced by electron donation from the ligands thus reducing the cal= culated =0Apartial atomic charge on the Fe centre.=0A=0AChanging the spin s= tate from either a singlet or a triplet (as I guess was your =0Ainitial mul= tiplicity) to a doublet WITHOUT changing (by one unit) the total =0Acharge = of the system will result in an error similar to that you obtained: with = =0Aan even number of electrons, one cannot under any circumstances have a d= oublet =0Aspin state (or a quartet or a sextet...). While MOZYME may have p= roblems with a =0Aradical system, this is not the error message that you ar= e getting.=0A=0AHope this helps,=0A=0AMark.=0A-----------------------------= ------------------------=0ADr. Mark Iron,=0AComputational Chemistry Unit,= =0ADepartment of Chemical Research Support,=0AKimmelman 251,=0AWeizmann Ins= titute of Science,=0ARehovot, Israel 76100.=0A=0ATel: +972 8 934 6218=0AFax= : +972 8 934 4142=0A=0Ae-mail: mark.a.iron~!~weizmann.ac.il=0Aweb: http://c= ompchem.weizmann.ac.il/ccu/=0A=0ANo trees were killed in the sending of thi= s message.=0AHowever, a large number of electrons were terribly inconvenien= ced.=0A=0A=0A=0A=0AOn Aug 2, 2011, at 5:15 PM, Goncalo Justino jgcj_+_fct.u= nl.pt wrote:=0A=0A> =0A> Sent to CCL by: "Goncalo Justino" [jgcj()fct.unl.p= t]=0A> =0A> =0A> oops...=0A> please forget my previous mail... mozyme does = not deal with radicals, as=0A> per the manual which i should re-read more o= ften...=0A> =0A> sorry for any waste of time,=0A> Gon=E7alo=0A> =0A> On Tue= , August 2, 2011 14:45, Goncalo Justino wrote:=0A>> Dear all,=0A>> =0A>> I'= m trying to do some jobs using MOZYME on a protein that contains a=0A>> Fe(= III) atom.=0A>> =0A>> The output of a 0scf indicates that the formal oxidat= ion state of Fe is=0A>> +2. In agreement with this, a job specifying a doub= let state, arising from=0A>> the Fe(III) atom 2-filled and 1-semi-filled or= bitals, fails to run with a=0A>> "DOUBLET SPECIFIED WITH EVEN NUMBER OF ELE= CTRONS, CORRECT FAULT".=0A>> =0A>> I've been playing around with most of mo= pac keywords [including=0A>> metal=3D(Fe), various cvb and setpi options], = but still fail to force it to=0A>> recognize Fe as Fe(III).=0A>> =0A>> Does= anyone have any suggestion or comment on this ?=0A>> =0A>> All the best,= =0A>> Gon=E7alo> =0A>=0A=0A=0A=0A-=3D This is automatically added to each m= essage by the mailing script =3D-=0ATo recover the email address of the aut= hor of the message, please change=0Athe strange characters on the top line = to the ^-^ sign. You can also=0Alook up the X-Original-From: line in the mail= header.=0A=0A=0A=A0 =A0 = =A0=0A=0AE-mail to administ= rators: CHEMISTRY-REQUEST^-^ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/c= gi-bin/ccl/send_ccl_message=0A=0A=0A=A0 =A0 =A0 http= ://www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait ti= me at: http://www.ccl.net=0A=0A=0AConferences:= http://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Mes= sages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail= bounces from CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www.ccl.net= /spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instructions= / --0-1536361414-1312451481=:35755 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Yes.
=0A
Goncalo's contribution should be use= ful for you. If a ligand is largely electron donating, it might a= lter the electronic configuration of the central metal (atom/ion)= without you knowing it. It is not physical! You are presuming a = d5 system, but the results were d6s for Fe. One or more ligand mi= ght have donated enough electron into the d-orbital of the Fe, es= pecially if the ligands have pi-electrons.
=0A
Hope this help= s.
 
Ol= asunkanmi Lukman Olawale
=0A
Current Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-Ife, Osun State.
Nigeria.
=0A
+234-0-80-52401564 Or +23= 4-0-80-67161091
=0A
=0A=0A

=0A

=0A
=0A
=0AFrom: Mark Iron= mark.a.iron a weizmann.ac.il <owner-chemistry^-^ccl.net>
To: "Olasunkanmi, Olawale Lukman -id#= 43q-" <walecomuk^-^yahoo.co.uk>
Sent: Tue, 2 August, 2011 8:20:04
Subject: CCL: mopac and mozype jobs with metal


Sent to CCL by: Mark Iron [mark.a.iron{}weizmann.ac.il]
Gon= =E7alo

I guess that you decided the the Fe as determined by MOZYME t= o be Fe(II) based in the partial atomic charge. Remember, that the definiti= on of Fe(III)/Fe(II) in an enzyme (or any other metal-organic system) is a = formality based on the ligands bound to it. With the type of ligands preval= ent in enzymes, it is not unexpected to find partial atomic charges signifi= cantly less than the formal metal oxidation state. Remember that atomic cha= rge and formal oxidation state are not physical observables but rather tools/aids we use = to help us understand the observed chemistry.  In your case, the forma= l +3 charge on Fe will be reduced by electron donation from the ligands thu= s reducing the calculated partial atomic charge on the Fe centre.

Ch= anging the spin state from either a singlet or a triplet (as I guess was yo= ur initial multiplicity) to a doublet WITHOUT changing (by one unit) the to= tal charge of the system will result in an error similar to that you obtain= ed: with an even number of electrons, one cannot under any circumstances ha= ve a doublet spin state (or a quartet or a sextet...). While MOZYME may hav= e problems with a radical system, this is not the error message that you ar= e getting.

Hope this helps,

Mark.
------------------------= -----------------------------
Dr. Mark Iron,
Computational Chemistry = Unit,
Department of Chemical Research Support,
Kimmelman 251,
Weizmann Institute of Science,
Rehovot, Israel 76100.

Te= l: +972 8 934 6218
Fax: +972 8 934 4142

e-mail: mark.a.iron~!~wei= zmann.ac.il
web: http://compchem.weizmann.ac.il/ccu/

No trees were kill= ed in the sending of this message.
However, a large number of electrons = were terribly inconvenienced.




On Aug 2, 2011, at 5:15 PM= , Goncalo Justino jgcj_+_fct.unl.pt wrote:

>
> Sent to CCL= by: "Goncalo Justino" [jgcj()fct.unl.pt]
>
>
> oops...=
> please forget my previous mail... mozyme does not deal with radica= ls, as
> per the manual which i should re-read more often...
> =
> sorry for any waste of time,
> Gon=E7alo
>
> On= Tue, August 2, 2011 14:45, Goncalo Justino wrote:
>> Dear all,>>
>> I'm trying to do some jobs using MOZYME on a protein that contains a
>> Fe(III) atom.
>>
>>= The output of a 0scf indicates that the formal oxidation state of Fe is>> +2. In agreement with this, a job specifying a doublet state, ari= sing from
>> the Fe(III) atom 2-filled and 1-semi-filled orbitals,= fails to run with a
>> "DOUBLET SPECIFIED WITH EVEN NUMBER OF ELE= CTRONS, CORRECT FAULT".
>>
>> I've been playing around w= ith most of mopac keywords [including
>> metal=3D(Fe), various cvb= and setpi options], but still fail to force it to
>> recognize Fe= as Fe(III).
>>
>> Does anyone have any suggestion or co= mment on this ?
>>
>> All the best,
>> Gon=E7al= o>
>



-=3D This is automatically added to each mess= age by the mailing script =3D-
To recover the email address of the autho= r of the message, please changelook up the X-Original-From: line in the ma= il header.

E-mail to subscribers: CHEMISTRY^-^ccl.net or use:
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=
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Before posting, check wait time = at: http://www.ccl.net<= BR>
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Search Messages: http://www.ccl.net/chemistr= y/searchccl/index.shtml

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--0-1536361414-1312451481=:35755-- From owner-chemistry@ccl.net Thu Aug 4 08:55:01 2011 From: "Olasunkanmi Lukman Olawale walecomuk::yahoo.co.uk" To: CCL Subject: CCL: Fw: CCL: mopac and mozype jobs with metal Message-Id: <-45203-110804063148-26943-YZoRLxUm2Sbl4h27X0VHig---server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-804041130-1312453899=:7617" Date: Thu, 4 Aug 2011 11:31:39 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk-.-yahoo.co.uk] --0-804041130-1312453899=:7617 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=A0Olasunkanmi Lukman Olawale=0A________________________________=0ACurre= nt Address:=0ADepartment of Chemistry,=0AObafemi Awolowo University,=0AIle-= Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-52401564 Or +234-0-80-67161091= =0A________________________________=0A=0A=0A=0A=0A----- Forwarded Message -= ---=0AFrom: Olasunkanmi Lukman Olawale =0ATo: CCL Su= bscribers =0ASent: Thu, 4 August, 2011 2:51:21=0ASubject= : Re: CCL: mopac and mozype jobs with metal=0AI wanted to say Mark Iron=0A= =0AYes.=0AMark's contribution should be useful for you. If a ligand=A0is la= rgely electron =0Adonating, it might=A0alter the electronic configuration= =A0of the central =0Ametal=A0(atom/ion) without=A0you knowing it.=A0It is n= ot physical! You are presuming a =0Ad5 system, but the results were d6s for= =A0Fe.=A0One or more ligand might =0Ahave=A0donated enough electron into th= e d-orbital of the Fe,=A0especially if =0Athe=A0ligands have pi-electrons.= =0AHope this helps.=0A=A0Olasunkanmi Lukman Olawale=0A_____________________= ___________=0ACurrent Address:=0ADepartment of Chemistry,=0AObafemi Awolowo= University,=0AIle-Ife, Osun State.=0ANigeria.=0A=0A+234-0-80-52401564 Or += 234-0-80-67161091=0A________________________________=0A=0A=0A=0A=0A=0A_____= ___________________________=0AFrom: Mark Iron mark.a.iron a weizmann.ac.il = =0ATo: "Olasunkanmi, Olawale Lukman " =0ASent: Tue, 2 August, 2011 8:20:04=0ASubject: CCL: mop= ac and mozype jobs with metal=0A=0A=0ASent to CCL by: Mark Iron [mark.a.iro= n{}weizmann.ac.il]=0AGon=E7alo=0A=0AI guess that you decided the the Fe as = determined by MOZYME to be Fe(II) based =0Ain the partial atomic charge. Re= member, that the definition of Fe(III)/Fe(II) in =0Aan enzyme (or any other= metal-organic system) is a formality based on the =0Aligands bound to it. = With the type of ligands prevalent in enzymes, it is not =0Aunexpected to f= ind partial atomic charges significantly less than the formal =0Ametal oxid= ation state. Remember that atomic charge and formal oxidation state =0Aare = not physical observables but rather tools/aids we use to help us understand= =0Athe observed chemistry.=A0 In your case, the formal +3 charge on Fe wil= l be =0Areduced by electron donation from the ligands thus reducing the cal= culated =0Apartial atomic charge on the Fe centre.=0A=0AChanging the spin s= tate from either a singlet or a triplet (as I guess was your =0Ainitial mul= tiplicity) to a doublet WITHOUT changing (by one unit) the total =0Acharge = of the system will result in an error similar to that you obtained: with = =0Aan even number of electrons, one cannot under any circumstances have a d= oublet =0Aspin state (or a quartet or a sextet...). While MOZYME may have p= roblems with a =0Aradical system, this is not the error message that you ar= e getting.=0A=0AHope this helps,=0A=0AMark.=0A-----------------------------= ------------------------=0ADr. Mark Iron,=0AComputational Chemistry Unit,= =0ADepartment of Chemical Research Support,=0AKimmelman 251,=0AWeizmann Ins= titute of Science,=0ARehovot, Israel 76100.=0A=0ATel: +972 8 934 6218=0AFax= : +972 8 934 4142=0A=0Ae-mail: mark.a.iron~!~weizmann.ac.il=0Aweb: http://c= ompchem.weizmann.ac.il/ccu/=0A=0ANo trees were killed in the sending of thi= s message.=0AHowever, a large number of electrons were terribly inconvenien= ced.=0A=0A=0A=0A=0AOn Aug 2, 2011, at 5:15 PM, Goncalo Justino jgcj_+_fct.u= nl.pt wrote:=0A=0A> =0A> Sent to CCL by: "Goncalo Justino" [jgcj()fct.unl.p= t]=0A> =0A> =0A> oops...=0A> please forget my previous mail... mozyme does = not deal with radicals, as=0A> per the manual which i should re-read more o= ften...=0A> =0A> sorry for any waste of time,=0A> Gon=E7alo=0A> =0A> On Tue= , August 2, 2011 14:45, Goncalo Justino wrote:=0A>> Dear all,=0A>> =0A>> I'= m trying to do some jobs using MOZYME on a protein that contains a=0A>> Fe(= III) atom.=0A>> =0A>> The output of a 0scf indicates that the formal oxidat= ion state of Fe is=0A>> +2. In agreement with this, a job specifying a doub= let state, arising from=0A>> the Fe(III) atom 2-filled and 1-semi-filled or= bitals, fails to run with a=0A>> "DOUBLET SPECIFIED WITH EVEN NUMBER OF ELE= CTRONS, CORRECT FAULT".=0A>> =0A>> I've been playing around with most of mo= pac keywords [including=0A>> metal=3D(Fe), various cvb and setpi options], = but still fail to force it to=0A>> recognize Fe as Fe(III).=0A>> =0A>> Does= anyone have any suggestion or comment on this ?=0A>> =0A>> All the best,= =0A>> Gon=E7alo> =0A>=0A=0A=0A=0A-=3D This is automatically added to each m= essage by the mailing script =3D-=0ATo recover the email address of the aut= hor of the message, please change=0Athe strange characters on the top line = to the : sign. You can also=0Alook up the X-Original-From: line in the mail= header.=0A=0A=0A=A0 =A0 = =A0=0A=0AE-mail to administ= rators: CHEMISTRY-REQUEST : ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/c= gi-bin/ccl/send_ccl_message=0A=0A=0A=A0 =A0 =A0 http= ://www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait ti= me at: http://www.ccl.net=0A=0A=0AConferences:= http://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Mes= sages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail= bounces from CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www.ccl.net= /spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instructions= / --0-804041130-1312453899=:7617 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A

 
Olasunkanmi Lukman Olawale=0A
=0ACurrent Address:
Department of Chemistry,
Ile-If= e, Osun State.
<= SPAN style=3D"COLOR: rgb(0,0,191); FONT-WEIGHT: bold">Nigeria.
=0A
+234-0-80-52401564 Or +234-0-80-67161091
=0A
=0A
=0A

=0A
=
=0A
----- Forwarded Message ----<= BR>From: Olasunkanmi Lukman= Olawale <walecomuk : yahoo.co.uk>
To: CCL Subscribers <chemistry : ccl.net>
Sent: Thu, 4 August, 2011 2:51:21
<= B>Subject: Re: CCL: mopac and = mozype jobs with metal
I wanted to say Mark Iron
=0A=0A
=0A
Yes.=0A
Mark's contribution should be useful for you. If a ligand is= largely electron donating, it might alter the electronic configuratio= n of the central metal (atom/ion) without you knowing it.&nb= sp;It is not physical! You are presuming a d5 system, but the results were = d6s for Fe. One or more ligand might have donated enough ele= ctron into the d-orbital of the Fe, especially if the ligands hav= e pi-electrons.
=0A
Hope this helps.
 
Olasunkanmi Lukman Olawale<= BR>=0A
=0ACurrent Address:
Department of Chemistry,
Obafemi Awolowo University,
Ile-I= fe, Osun State.
= Nigeria.
=0A
+234-0-80-52401564 Or +234-0-80-67161091
=0A=0A
=0A

=0A

=0A
=0A
=0AFrom: Mark Iron mark.a.iron a weizmann.ac.il &l= t;owner-chemistry : ccl.net>
To: "Olasunkanmi, Olawale Lukman " <walecomuk : yahoo.co.uk&= gt;
Sent: Tue, 2 August,= 2011 8:20:04
Subject: C= CL: mopac and mozype jobs with metal


Sent to CCL by: Mark= Iron [mark.a.iron{}weizmann.ac.il]
Gon=E7alo

I guess that you de= cided the the Fe as determined by MOZYME to be Fe(II) based in the partial = atomic charge. Remember, that the definition of Fe(III)/Fe(II) in an enzyme= (or any other metal-organic system) is a formality based on the ligands bo= und to it. With the type of ligands prevalent in enzymes, it is not unexpec= ted to find partial atomic charges significantly less than the formal metal= oxidation state. Remember that atomic charge and formal oxidation state are not physical observables but rather tools/aids we use = to help us understand the observed chemistry.  In your case, the forma= l +3 charge on Fe will be reduced by electron donation from the ligands thu= s reducing the calculated partial atomic charge on the Fe centre.

Ch= anging the spin state from either a singlet or a triplet (as I guess was yo= ur initial multiplicity) to a doublet WITHOUT changing (by one unit) the to= tal charge of the system will result in an error similar to that you obtain= ed: with an even number of electrons, one cannot under any circumstances ha= ve a doublet spin state (or a quartet or a sextet...). While MOZYME may hav= e problems with a radical system, this is not the error message that you ar= e getting.

Hope this helps,

Mark.
------------------------= -----------------------------
Dr. Mark Iron,
Computational Chemistry = Unit,
Department of Chemical Research Support,
Kimmelman 251,
Weizmann Institute of Science,
Rehovot, Israel 76100.

Te= l: +972 8 934 6218
Fax: +972 8 934 4142

e-mail: mark.a.iron~!~wei= zmann.ac.il
web: http://compchem.weizmann.ac.il/ccu/

No t= rees were killed in the sending of this message.
However, a large number= of electrons were terribly inconvenienced.




On Aug 2, 20= 11, at 5:15 PM, Goncalo Justino jgcj_+_fct.unl.pt wrote:

>
&g= t; Sent to CCL by: "Goncalo Justino" [jgcj()fct.unl.pt]
>
> > oops...
> please forget my previous mail... mozyme does not de= al with radicals, as
> per the manual which i should re-read more oft= en...
>
> sorry for any waste of time,
> Gon=E7alo
&g= t;
> On Tue, August 2, 2011 14:45, Goncalo Justino wrote:
>>= ; Dear all,
>>
>> I'm trying to do some jobs using MOZYME on a protein that contains a
>> Fe(III) atom.
>> =
>> The output of a 0scf indicates that the formal oxidation state= of Fe is
>> +2. In agreement with this, a job specifying a double= t state, arising from
>> the Fe(III) atom 2-filled and 1-semi-fill= ed orbitals, fails to run with a
>> "DOUBLET SPECIFIED WITH EVEN N= UMBER OF ELECTRONS, CORRECT FAULT".
>>
>> I've been play= ing around with most of mopac keywords [including
>> metal=3D(Fe),= various cvb and setpi options], but still fail to force it to
>> = recognize Fe as Fe(III).
>>
>> Does anyone have any sugg= estion or comment on this ?
>>
>> All the best,
>&= gt; Gon=E7alo>
>



-=3D This is automatically added = to each message by the mailing script =3D-
To recover the email address = of the author of the message, please changelook up the X-Original-From: l= ine in the mail header.

E-mail to subscribers: CHEMISTRY : ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to ad= ministrators: CHEMISTRY-REQUE= ST : ccl.net or use
      http://www.cc= l.net/cgi-bin/ccl/send_ccl_message
&n= bsp;     http://www.ccl.net/chemistry/sub_unsub.shtm= l

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/a= nnouncements/conferences/

Search Messages: ht= tp://www.ccl.net/chemistry/searchccl/index.shtml

If your mail bo= unces from CCL with 5.7.1 error, check:
      http://www.= ccl.net/spammers.txt

RTFI: http://www.ccl.ne= t/chemistry/aboutccl/instructions/


=0A
--0-804041130-1312453899=:7617-- From owner-chemistry@ccl.net Thu Aug 4 12:39:00 2011 From: "Alex Allardyce aa[A]chemaxon.hu" To: CCL Subject: CCL: Program announcement and call for participants: ChemAxon's 2011 UGM: September 27-28,San Diego, CA Message-Id: <-45204-110804123155-17564-h6P+rXqnKPKWX/+o5pWWbA]=[server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 Aug 2011 18:32:01 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa||chemaxon.hu] Good day, We are announcing the program and calling for participants for ChemAxon's 4th US User Group Meeting (US-UGM) which will take place in San Diego, CA on September 27-28. Program: http://www.chemaxon.com/events/ugm-san-diego-2011/#program Highlights of the event: 1. Program is launched with presentations from users including; Boehringer Ingelheim, Broad Inst, GlaxoSmithKline, NCTT, NextMove Software, Pfizer, RTI Int., Takeda, Thomson Reuters, full presentation titles below. 2. Preceding the meeting on Monday afternoon, Sept 26, we host a dedicated Markush Forum, sponsored by Thomson Reuters, a free session - for content users to discuss the development and use of Markush structure IP tools and content. 3. Following the meeting on Thursday Sept 29, will be a two track Training Day for: Application and Developer, for beginner to advanced level users to become familiar with ChemAxon's toolkits and end user applications. 4. A relaxing location and many social events to mix in and enjoy Useful links: Program: http://www.chemaxon.com/events/ugm-san-diego-2011/#program More information: http://www.chemaxon.com/events/2011_eugm/ Registration: http://www.chemaxon.com/events/ugm-registration/ Markush Forum: http://www.chemaxon.com/events/ugm-san-diego-2011/#markush Developer training details: http://www.chemaxon.com/events/ugm-san-diego-2011/#developer Application training details: http://www.chemaxon.com/events/ugm-san-diego-2011/#appfocus UGM archives: http://www.chemaxon.com/ugm-presentations/ Program titles: User Presentations 01 QnA and Keynote: Surviving the whitewater of R&D Informatics: How can we best support science in an ever-changing world 02 ZINC-12: A tool for the discovery, prioritization and acquisition of commercially available small molecule reagents for biology. 03 A novel Approach to Pharmaceutical Registration - Registration as a Service 04 Implementation of an Integrated Cheminformatics System at RTI 05 The Evolution of the Broad Chemical Biology Informatics Platform 06 Development and Deployment of Reagent Logistics Solution Using JChem Base/Cartridge 07 Centralizing data for drug discovery in a multi-group academic setting with ChemAxon 08 Enterprise Deployment of JChem for Excel (JC4XL) 09 Deploying Instant JChem on an Enterprise Scale 10 Excel as a Cheminformatics Interface 11 Efficient simultaneous matching of multiple SMARTS using the ChemAxon toolkits 12 Advanced searching chemical structures in patents 13 Tools for Analyzing Exemplified and Markush Structures in Chemical Patents 14 Reaction scheme: Capture, Iterator, and Parser 15 Smashing Molecules - How Molecular Fragments Allow us to Explore Large Chemical Spaces 16 Text mining for chemical information: the ChiKEL project Advisory: Event hotel has reservation cut-off date of 24th of August. Accommodation can be booked here: https://shop.evanshotels.com/catamaran_groups/chemaxon1109507.html See you in September. ChemAxon From owner-chemistry@ccl.net Thu Aug 4 13:31:00 2011 From: "Eli Lam eli_lsh()yahoo.com.hk" To: CCL Subject: CCL:G: transition dipole moment Message-Id: <-45205-110804120226-26489-WJy+UJoSANc1C++D5LzL0Q**server.ccl.net> X-Original-From: "Eli Lam" Date: Thu, 4 Aug 2011 12:02:22 -0400 Sent to CCL by: "Eli Lam" [eli_lsh,yahoo.com.hk] Hi CCLers, I have some queries to the basic of transition dipole moment and would like to ask what exactly is transition dipole moment? Is it equalled to the dipole moment difference between the ground state and the excited state of a molecule? Or how to calculate it using gaussian03 package? And is it related to the probability of the transition to a particular excited state? Thank you so much! Eli From owner-chemistry@ccl.net Thu Aug 4 16:28:00 2011 From: "Victor Rosas Garcia rosas.victor,,gmail.com" To: CCL Subject: CCL: dft for radicals? Message-Id: <-45206-110804161630-20492-Vn635zLIjODI6fSDeFSUIQ,,server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 4 Aug 2011 15:16:21 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor[A]gmail.com] Hello everybody, I looking for a functional suitable for radicals (phenoxy type) for the calculation of bond dissociation energies and spin densities. So far my library search has not turned up much. Of course, I have found a ton of dft studies on radicals, but no review that discusses the relative merits of different functionals for this kind of calculation. Can anyone point to a review of this kind? Thanx for your attention Victor From owner-chemistry@ccl.net Thu Aug 4 17:06:00 2011 From: "Oellien, F \(Frank\) frank.oellien/./msd.de" To: CCL Subject: CCL: GCC2011: Extended Submission Deadline / Last Call for Paper Message-Id: <-45207-110804162256-3760-biH/79e7en1uwlNl2OIuVw*_*server.ccl.net> X-Original-From: "Oellien, F \(Frank\)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 4 Aug 2011 22:22:42 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F \(Frank\)" [frank.oellien*_*msd.de] Last CALL FOR PAPERS Extended Deadline for Submission 7th German Conference on Chemoinformatics (GCC2011) 6 - 8 November 2011 Dear Colleague, As already announced in our invitation flyer the "7th German Conference on Chemoinformatics" (http://www.gdch.de/vas/tagungen/tg/5227_einladung.pdf) of the GDCh Division Chemistry-Information-Computer will take place in Goslar/Germany from November 6 - 8, 2011. The deadline for submitting abstracts has been extended! We kindly invite you to submit your abstract until August 15, 2011. (http://www.gdch.de/gcc2011) to be held in Goslar, Germany, November 6 - 8, 2011. Topics of the conference are: * Chemoinformatics and Drug Discovcery * Chemical Information, Patents, and Databases * Molecular Modelling * Computational Material Science and Nanotechnology In addition other highlights in the field of Computational Chemistry are also welcome. For information on scholarships, please visit the conference webpage or note the special section in the invitation (http://www.gdch.de/vas/tagungen/tg/5227_einladung.pdf). Confirmed Plenary Speakers are: * Johann Gasteiger, University of Erlangen/Molecular Networks, Erlangen, DE * Oliver Kohlbacher, University of Tübingen, DE * Eva Rauls, University of Paderborn, DE * Herbert Koeppen, Boehringer Ingelheim, Biberach, DE * Colin Batchlor, RCS, London, UK * Colin Groom, CCDC, Cambridge, UK * Xavier Barril, University of Barcelona, ES * Secret Guest Speaker from MIT! Visit the conference website at www.gdch.de/gcc2011 for more information or access directly the Call-for-Paper PDF http://www.gdch.de/vas/tagungen/tg/5227_einladung.pdf Frank Oellien Chairman GDCh CIC Division Mit freundlichen Grüßen / With kind regards Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien%x%msd.de Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.msd-animal-health.de Hinweis: Diese Email wird von einem Unternehmen der deutschen MSD-Gruppe versandt. Hierzu gehören folgende Vertriebsunternehmen: Humanarzneimittel: MSD Sharp & Dohme GmbH, Lindenplatz 1, 85540 Haar; HR München B 64194 Geschäftsführer: Hanspeter Quodt (Vors.), Dr. Claus Dollinger, Dr. Thomas Lang, Dr. Veit Stoll Aufsichtsratsvorsitzender: Dr. Diethard Solderer Tierarzneimittel: Intervet Deutschland GmbH, Feldstr. 1a, 85716 Unterschleißheim; HR München B 138151 Geschäftsführer: Dr. Daniel Sicher Weitere Unternehmen der deutschen MSD-Gruppe siehe http://info.msd.de/pflichtangaben From owner-chemistry@ccl.net Thu Aug 4 17:41:00 2011 From: "Alcides Simao alsimao#,#gmail.com" To: CCL Subject: CCL: dft for radicals? Message-Id: <-45208-110804170915-9935-z8DuPTgYSx8DhEYWAqaO/g=-=server.ccl.net> X-Original-From: Alcides Simao Content-Type: multipart/alternative; boundary=001517588c6435ca8a04a9b464f5 Date: Thu, 4 Aug 2011 22:09:07 +0100 MIME-Version: 1.0 Sent to CCL by: Alcides Simao [alsimao*gmail.com] --001517588c6435ca8a04a9b464f5 Content-Type: text/plain; charset=ISO-8859-1 Hi Victor, See if this interests you! http://cat.inist.fr/?aModele=afficheN&cpsidt=13801153 Best, Alcides --001517588c6435ca8a04a9b464f5 Content-Type: text/html; charset=ISO-8859-1 Hi Victor,

See if this interests you!

http://cat.inist.fr/?aModele=afficheN&cpsidt=13801153

Best,

Alcides
--001517588c6435ca8a04a9b464f5-- From owner-chemistry@ccl.net Thu Aug 4 19:18:01 2011 From: "Victor Rosas Garcia rosas.victor++gmail.com" To: CCL Subject: CCL: dft for radicals? Message-Id: <-45209-110804191633-22782-r1xM0PObESvsYnftDmXmiw.:.server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 4 Aug 2011 18:16:24 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor.++.gmail.com] It certainly does! I'll see if I can get the paper. thanx 2011/8/4 Alcides Simao alsimao#,#gmail.com : > Hi Victor, > > See if this interests you! > > http://cat.inist.fr/?aModele=afficheN&cpsidt=13801153 > > Best, > > Alcides >