From owner-chemistry@ccl.net Thu Sep 27 00:56:01 2012 From: "Mark Zottola mzottola[]gmail.com" To: CCL Subject: CCL: Mills-Nixon effect Message-Id: <-47677-120926170757-6155-3Bgv28Vz/0h018aNY8dyaA#%#server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=e89a8f23585f3ec46104caa13780 Date: Wed, 26 Sep 2012 17:07:52 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola-#-gmail.com] --e89a8f23585f3ec46104caa13780 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Because, as I noted earlier, Mills Nixon is bond fixation to avoid the negative energetic consequences of an anti-aromatic system. Substituents do not cause bond fixation. Nor do they change whether a system is aromatic or anti-aromatic. They do not fundamentally change the symmetry of the MOs nor do they make a system less anti-aromatic. While reactivity of a system changes due to substiuent effects, the system itself does not inherently become more stable because of a substituent. Mills-Nixon deals only with the stabilization of anti-aromatic systems. What you propose has nothing to do with that. On Wed, Sep 26, 2012 at 2:09 PM, Sergio Manzetti sergio.manzetti ~ gmx.com = < owner-chemistry : ccl.net> wrote: > Mark, in a paper by Verdal and Hudson, Chemical Physics Letters 434 (2007= ) > 241=96244, the Mills Nixon effect is described the change in reactivity > caused by the localization of the benzene double-bonds. If the > localization of pi bonds changes reactivity, why cannot other functional > groups that alter the distribution of aromatic bonds in a ring still be > regarded as Mills Nixon? The reactivity must change if the electronic > density is affected (Fukui, 1982). Thus, why cannot any functional group > that affects the subdivision of bonds in a benzene be called Mills-Nixon? > > Sergio > > > > ----- Original Message ----- > > From: Mark Zottola mzottola**gmail.com > > Sent: 09/26/12 03:36 PM > > To: Manzetti, Sergio > > Subject: CCL: Mills-Nixon effect > > The Mills-Nixon effect, that of bond fixation - does not depend on any > annulation onto a benzene ring or any aromatic system. Rather it is a > breaking of symmetry of the pi system to avoid the destabilization of an > anti-aromatic system, i;e., those systems with 4n pi electrons. THis > apparently also extends to molecules with 4n+2 pi electrons containing an > anti-aromatic substructure. > > Biphenylene is an appropriate example. Two benzene rings are bonded > together each at the 1,2 positions, defining a 4-membered ring between > them. Considering the resonance contributing structures, one sees that t= he > 4-membered ring can contain 2 pi bonds - and is therefore a cyclobutadien= yl > substructure. As the entire molecule contains 12 pi electrons, the fully > conjugated system would be anti-aromatic as well. The Mills-Nixon effect > breaks the overall symmetry of the system by lengthening the bonds betwee= n > the two benzene rings. That bond elongation isolates the two benzene rin= gs > and avoids the destabilization of a fully-conjugated anti aromatic system= . > Therefore, the Mills-Nixon effect disrupts the conjugation of the system > to achieve stability. > > When one attaches substituents to an aromatic system, there is no change > in the number of pi electrons in the ring system. Therefore attaching a > methoxy group to benzene does not change the aromaticity of the benzene > system. Similarly, adding a nitro group to cyclobutadiene does not chang= e > the number of pi electrons in the system (4) and therefore the system > remains anti-aromatic. There will be changes to the bond lengths in any > cyclic, conjugated system by the addition of any substituent, be it > methoxy, nitro, fluoro, amino, etc. Those changes reflect the perturbati= on > of the MO energy levels by the substituent, but they are not disrupting t= he > conjugation in the overall system. Therefore, these are not an aspect of > the Mills-Nixon effect. > > > > On Wed, Sep 26, 2012 at 6:46 AM, Sergio Manzetti sergio.manzetti!^! > gmx.com wrote: > >> Dear CCLrs, does the Mills-Nixon effect unilaterally depend on the >> annelation of four, five or six-membered rings onto benzene giving and >> alternation of reactivity, or does the effect also encomapss: >> >> - linking of ANY functional group to an aromatic unit? >> >> Thanks >> >> Sergio > > > > > > --e89a8f23585f3ec46104caa13780 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Because, as I noted earlier, Mills Nixon is bond fixation to avoid the nega= tive energetic consequences of an anti-aromatic system. =A0Substituents do = not cause bond fixation. =A0Nor do they change whether a system is aromatic= or anti-aromatic. =A0They do not fundamentally change the symmetry of the = MOs nor do they make a system less anti-aromatic. =A0While reactivity of a = system changes due to substiuent effects, the system itself does not inhere= ntly become more stable because of a substituent.

Mills-Nixon deals only with the stabilization of anti-aromat= ic systems. =A0What you propose has nothing to do with that.

On Wed, Sep 26, 2012 at 2:09 PM, Sergio Manzetti sergio= .manzetti ~ gmx.com <owner-chemistry : = ccl.net> wrote:
=20 Mark, i= n a paper by Verdal and Hudson, Chemical Physics Letters 434 (2007) 241=962= 44, the Mills Nixon effect is described the change in reactivity caused by = the localization of the benzene double-bonds.=A0 If the localization of pi = bonds changes reactivity, why cannot other functional groups that alter the= distribution of aromatic bonds in a ring still be regarded as Mills Nixon?= The reactivity must change if the electronic density is affected (Fukui, 1= 982). Thus, why cannot any functional group that affects the subdivision of= bonds in a benzene be called Mills-Nixon?
=20
=20 Sergio
=20
=20

=20 =A0

=20
=20

=20 ----- Origina= l Message -----

=20

=20 From: Mark Zo= ttola mzottola**gmail.com

=20

=20 Sent: 09/26/1= 2 03:36 PM

=20

=20 To: Manzetti,= Sergio

=20

=20 Subject: CCL:= Mills-Nixon effect

= =20
=20
=20

=20 The = Mills-Nixon effect, that of bond fixation - does not depend on any annulati= on onto a benzene ring or any aromatic system. =A0Rather it is a breaking o= f symmetry of the pi system to avoid the destabilization of an anti-aromati= c system, i;e., those systems with 4n pi electrons. =A0THis apparently also= extends to molecules with 4n+2 pi electrons containing an anti-aromatic su= bstructure.=A0

=20
=20 =A0<= /span>
=20
=20 Biph= enylene is an appropriate example. =A0Two benzene rings are bonded together= each at the 1,2 positions, defining a 4-membered ring between them. =A0Con= sidering the resonance contributing structures, one sees that the 4-membere= d ring can contain 2 pi bonds - and is therefore a cyclobutadienyl substruc= ture. =A0As the entire molecule contains 12 pi electrons, the fully conjuga= ted system would be anti-aromatic as well. =A0The Mills-Nixon effect breaks= the overall symmetry of the system by lengthening the bonds between the tw= o benzene rings. =A0That bond elongation isolates the two benzene rings and= avoids the destabilization of a fully-conjugated anti aromatic system. =A0= Therefore, the Mills-Nixon effect disrupts the conjugation of the system to= achieve stability.
=20
=20 =A0<= /span>
=20
=20 When= one attaches substituents to an aromatic system, there is no change in the= number of pi electrons in the ring system. =A0Therefore attaching a methox= y group to benzene does not change the aromaticity of the benzene system. = =A0Similarly, adding a nitro group to cyclobutadiene does not change the nu= mber of pi electrons in the system (4) and therefore the system remains ant= i-aromatic. =A0There will be changes to the bond lengths in any cyclic, con= jugated system by the addition of any substituent, be it methoxy, nitro, fl= uoro, amino, etc. =A0Those changes reflect the perturbation of the MO energ= y levels by the substituent, but they are not disrupting the conjugation in= the overall system. =A0Therefore, these are not an aspect of the Mills-Nix= on effect.
=20
=20 =A0<= /span>
=20
=20
=20
=20
=20 On = Wed, Sep 26, 2012 at 6:46 AM, Sergio Manzetti sergio.manzetti!^!gmx.com <owner-chemistry*ccl.net> wrote:
=20
=20 Dear CCLrs= , does the Mills-Nixon effect unilaterally depend on the annelation of four= , five or six-membered rings onto benzene giving and alternation of reactiv= ity,=A0 or does the effect also encomapss:
=20
=20 - linking of ANY functional group to an aromatic unit?
=20
=20 Thanks
=20
=20 Sergio
=20
=20
=20
=20
=20

=20 =A0

=20
=20
=20 =A0
=20

--e89a8f23585f3ec46104caa13780-- From owner-chemistry@ccl.net Thu Sep 27 03:06:00 2012 From: "Michel Petitjean petitjean.chiral_+_gmail.com" To: CCL Subject: CCL: Symmetry Message-Id: <-47678-120927030404-21516-ViYhs617jaNeakZnzoInLw\a/server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 27 Sep 2012 09:03:54 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral]_[gmail.com] Dear Will, I did some work in quasi-symmetry measurements (see my freeware QCM, URL below). I would be delighted to learn about the algorithm which "symmetrizes the structure". Can you give me the references ? Thanks. Michel. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral-$-gmail.com (preferred), michel.petitjean-$-univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#QCM 2012/9/26 William F. Polik polik]-[hope.edu : > ... > > WebMO (www.webmo.net) can identify the point group of any molecule, and also > the subgroups. Furthermore, if the molecule is "nearly symmetric," it can > identify the nearest point group and subgroups, and then symmetrize the structure as requested. > ... From owner-chemistry@ccl.net Thu Sep 27 05:00:00 2012 From: "AMBRISH KUMAR SRIVASTAVA ambrishphysics]-[gmail.com" To: CCL Subject: CCL: Computational Chemistry congress in Barcelona Message-Id: <-47679-120927045905-30578-pYOtgs2OUgszAPvEvu8cng ~~ server.ccl.net> X-Original-From: AMBRISH KUMAR SRIVASTAVA Content-Type: multipart/alternative; boundary=14dae9340b45701b6c04caab25a4 Date: Thu, 27 Sep 2012 14:28:43 +0530 MIME-Version: 1.0 Sent to CCL by: AMBRISH KUMAR SRIVASTAVA [ambrishphysics^gmail.com] --14dae9340b45701b6c04caab25a4 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sir/Madam The 7th* Workshop on Computational Chemistry and Its Applications (7th CCA) will be organized as part of the International Conference on Computational Science (ICCS 2013).* ICCS 2013 will be held from 5 to 7 June 2013 in Barcelona. http://www.iccs-meeting.org/iccs2013/index.html You are invited to submit full paper/s to be considered for the 7th CCA workshop. Prof John Dyke from the University of Southampton will deliver the keynote address entitled "Probing the structure and reactivity of Reactive Intermediates with Photoionization and Quantum Chemistry calculations". All details are available on workshop webpage, http://sites.uom.ac.mu/cca/ All papers will be peer-reviewed and accepted papers (oral or poster) will be published in Procedia Computer Science ( http://www.elsevier.com/wps/find/journaldescription.cws_home/719435/descrip= tion ) Let me know if you need any more information. Looking forward to receive your full paper/s. Kind regards. Prof Ponnadurai Ramasami 7th CCA Workshop Organizer *Professor Ponnadurai Ramasami** *|* *FRSC, FICCE, CSci, CChem | ?Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, R=E9duit, Mauritius | Tel: ) +230 403-7506 | Fax: = 6 +230 465-6928 | | + ramchemi*o*intnet.mu | =FF www.uom.ac.mu | =FF www.uom.ac.mu/sites/CCUOM/index.html | *< Chemistry I Computational I Chemistry > =3D Useful results < Chemistry I Chemistry >* =FC Please think about the environment. Print this email only if required. P* *Think green. Think before you print. On Thu, Sep 27, 2012 at 7:44 AM, Dr. Daniel Glossman-Mitnik dglossman[A] gmail.com wrote: > > Sent to CCL by: "Dr. Daniel Glossman-Mitnik" [dglossman]-[gmail.com] > Dear all: > > I have received an e-mail with the announcement of a Computational > Chemistry related congress to be held in Barcelona, Spain during 2013. > However, unfortunately I have deleted the message. May somebody send me > information about this? > > Thanks in advance. Best regards, > > Daniel > > > ************************************************************************ > Dr. Daniel Glossman-Mitnik > NANOCOSMOS Virtual Lab - CIMAV, SC > Miguel de Cervantes 120 - Comp. Ind. Chihuahua > Chihuahua, Chih 31109 - M=E9xico > Tel: 614 4391151. Lab: 614 4394805/1190 > Secretar=EDa/FAX: 614 4391130 > Corro electr=F3nico: daniel.glossman!A!cimav.edu.mx > dglossman!A!gmail.com > P=E1gina WEB: http://www.cimav.edu.mx/cv/daniel.glossman > ************************************************************************ > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 *Ambrish K. Srivastava CSIR Junior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007* --14dae9340b45701b6c04caab25a4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Sir/Madam

The 7th Workshop= on Computational Chemistry and Its Applications (7th CCA) will be organized as part of the International Conference on Computational Science (ICCS 2013).

ICCS 2013 will be h= eld from 5 to 7 June 2013 in Barcelona.

http://www.iccs-meeting.org/iccs2013/index.html=

You are invited to = submit full paper/s to be considered for the 7th CCA workshop. <= /p>

=A0

Prof John Dyke from the University of Southampton will deliver the keynote address entitled "Probing the structure and reactivity of Reactive Intermediates with Photoionization and Quantum Chemistry calculations".

=A0

All details are ava= ilable on workshop webpage, http://sites.uom.ac.mu/cca= /

All papers will be = peer-reviewed and accepted papers (oral or poster) will be published in Procedia Computer Science (http://www.elsevier.com/wps/find/journaldescription.cws_home/7194= 35/description)

Let me know if you = need any more information.

Looking forward to = receive your full paper/s.

Kind regards.

Prof Ponnadurai Ram= asami

=A0

7th CCA = Workshop Organizer

=A0Professor Ponnadurai Ramasami | FRSC, FICCE, CSci, CChem | ? Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, R=E9duit, Mauritiu= s | Tel: )230 403-7506 | Fax: 6 +230 4= 65-6928 | | +=A0ramchemi*o*intnet.mu |= =FF <= a href=3D"http://www.uom.ac.mu/" target=3D"_blank">www.uom.ac.mu= | =FF www.uom.ac.mu/sites/CCUOM/index.html<= span style=3D"font-size:10.0pt;font-family:"Arial","sans-ser= if""> |

< Chemistry I Computational I Chemistry > =3D Useful results < Chemistr= y I Chemistry >

=FC Please think about the environment. Print this email only if required.=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0

P=A0 Think green. Think before you = print.

=A0

On Thu, Sep 27, 2012 at 7:44 AM, Dr. Dan= iel Glossman-Mitnik dglossman[A]gmail.com = <owner-chemistry[#]ccl.net> wrote:

Sent to CCL by: "Dr. Daniel Glossman-Mitnik" [dglossman]-[gmail.com]
Dear all:

I have received an e-mail with the announcement of a Computational Chemistr= y related congress to be held in Barcelona, Spain during 2013. However, unf= ortunately I have deleted the message. May somebody send me information abo= ut this?

Thanks in advance. Best regards,

Daniel


************************************************************************ Dr. Daniel Glossman-Mitnik
NANOCOSMOS Virtual Lab - CIMAV, SC
Miguel de Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih 31109 - M=E9xico
Tel: 614 4391151. =A0Lab: 614 4394805/1190
Secretar=EDa/FAX: =A0614 4391130
Corro electr=F3nico: =A0daniel.glossman!A!cimav.edu.mx
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 dglossman!A!gmail.com
P=E1gina WEB: =A0http://www.cimav.edu.mx/cv/daniel.glossman
************************************************************************


-=3D This is automatically added to each message by the mailing script =3D-=
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--
Ambrish K. Srivastava
CSIR Junior Research Fellow
Depar= tment of Physics
University of Lucknow
Lucknow, India-226007=
--14dae9340b45701b6c04caab25a4-- From owner-chemistry@ccl.net Thu Sep 27 08:18:00 2012 From: "Marcel Swart marcel.swart:icrea.cat" To: CCL Subject: CCL: Symmetry Message-Id: <-47680-120927032147-28033-fpkNlJJo5oGbsGY5X01a4w() server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary="Apple-Mail=_35D97843-AECD-489B-8AAC-C9EBEDDB79F5" Date: Thu, 27 Sep 2012 09:21:37 +0200 Mime-Version: 1.0 (Mac OS X Mail 6.1 \(1498\)) Sent to CCL by: Marcel Swart [marcel.swart-*-icrea.cat] --Apple-Mail=_35D97843-AECD-489B-8AAC-C9EBEDDB79F5 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 See previous posts in the CCL list, for instance the one about symmol: http://www.ccl.net/cgi-bin/ccl/message-new?2008+01+31+010 The symmol program and description can be found at: http://web.chem.ucsb.edu/~kalju/chem226/public/pcgamess_tutorial_A2.html Marcel On Sep 26, 2012, at 14:48 , William F. Polik polik]-[hope.edu = wrote: > Sergio, >=20 > WebMO (www.webmo.net) can identify the point group of any molecule, = and also the subgroups. Furthermore, if the molecule is "nearly = symmetric," it can identify the nearest point group and subgroups, and = then symmetrize the structure as requested. Finally, for educational = purposes, it can display the symmetry elements on the molecule. >=20 > Although you can download and install WebMO for free, it is simpler = just to try it out by visiting the Working Demo webpage: > www.webmo.net/demo > You could import your structure with New Job: Import Job, and then = choose Symmetry: Symmetrize to display the point group and subgroups. = Choosing Symmetry: Display Symmetry Elements will do the obvious. >=20 > The algorithms used by WebMO have been published in: R. Jeffrey = Largent, William F. Polik, and J.R. Schmidt, "Symmetrizer: Algorithmic = Determination of Point Groups in Nearly Symmetric Molecules," Journal of = Computational Chemistry 33, 1637-42 (2012). >=20 > The WebMO symmetry feature has been very useful not only for detecting = symmetry in complex molecules, but also for symmetrizing nearly = symmetric molecules and for teaching symmetry and point groups to = students. >=20 > Will Polik >=20 > On 9/21/12 12:13 PM, Sergio Manzetti sergio.manzetti^^gmx.com wrote: >> Dear CCLrs, it is evident that molecular symmetry is not straight = forward for complex molecules. Are there any computational methods to = determine the symmetry of an input structure, and its subgroups? >>=20 >> Sergio >=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart.() .icrea.cat marcel.swart.() .udg.edu web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail=_35D97843-AECD-489B-8AAC-C9EBEDDB79F5 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 See = previous posts in the CCL list, for instance the one about = symmol:

The symmol program and description can be found at:

Marcel

On = Sep 26, 2012, at 14:48 , William F. Polik polik]-[hope.edu <owner-chemistry.() .ccl.net> = wrote:

=20 =20
Sergio,

WebMO (www.webmo.net) can identify the point = group of any molecule, and also the subgroups.  Furthermore, if the molecule is = "nearly symmetric," it can identify the nearest point group and subgroups, and then symmetrize the structure as requested.  Finally, for educational purposes, it can display the symmetry elements on the molecule.

Although you can download and install WebMO for free, it is simpler just to try it out by visiting the Working Demo webpage:
    www.webmo.net/demo
You could import your structure with New Job: Import Job, and then choose Symmetry: Symmetrize to display the point group and subgroups.  Choosing Symmetry: Display Symmetry Elements will = do the obvious.

The algorithms used by WebMO have been published in:  R. = Jeffrey Largent, William F. Polik, and J.R. Schmidt, "Symmetrizer: Algorithmic Determination of Point Groups in Nearly Symmetric Molecules," Journal of Computational Chemistry 33, 1637-42 = (2012).

The WebMO symmetry feature has been very useful not only for detecting symmetry in complex molecules, but also for symmetrizing nearly symmetric molecules and for teaching symmetry and point groups to students.

Will Polik

On 9/21/12 12:13 PM, Sergio Manzetti sergio.manzetti^^gmx.com wrote:
Dear CCLrs, it is evident that molecular symmetry is not straight forward for complex molecules. Are there any computational methods to determine the symmetry of an input structure, and its subgroups?

Sergio



=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
dr. = Marcel Swart

ICREA Research Professor at
Institut de Qu=EDmica = Computacional
Universitat de Girona

Facultat de = Ci=E8ncies
Campus Montilivi
17071 = Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart.() .icrea.cat
marce= l.swart.() .udg.edu
web
http://www.marcelswart.eu

vCard
addressbook://www.mar= celswart.eu/MSwart.vcf
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

= --Apple-Mail=_35D97843-AECD-489B-8AAC-C9EBEDDB79F5-- From owner-chemistry@ccl.net Thu Sep 27 12:09:00 2012 From: "James T Metz James.Metz[a]Abbott.com" To: CCL Subject: CCL: Non QM Descriptor based models to predict redox potentials Message-Id: <-47681-120927120446-30388-rhXaKTe4N1/tpXOmN6VPyQ###server.ccl.net> X-Original-From: "James T Metz" Date: Thu, 27 Sep 2012 12:04:45 -0400 Sent to CCL by: "James T Metz" [James.Metz.:.Abbott.com] CCL Members, Is anyone aware of any publications describing the construction of models to predict redox potentials of diverse small molecules that do not involve QM, DFT, or semi-empirical calculations or descriptors derived from those calculations? Hence, if such models exist they would likely utilize aromatic rings, topology of conjugated bonds and adjacent functional groups, etc. If no such publications exist, is anyone aware of databases of small molecules with experimentally measured redox potentials. I have already tried Google without success other than finding QM publns, etc. I am trying to avoid using these methods because I want to be able to perform calculations for large sets of compounds (1000's of small molecules) and obtain rough, but reasonable estimates of the redox potentials. Thank you. Regards, Jim Metz Abbott Laboratories From owner-chemistry@ccl.net Thu Sep 27 13:43:00 2012 From: "Jason Cole cole[A]ccdc.cam.ac.uk" To: CCL Subject: CCL: Symmetry Message-Id: <-47682-120927102321-16819-um9ozBcK9E1rKYb57GepSg[-]server.ccl.net> X-Original-From: Jason Cole Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 27 Sep 2012 15:23:08 +0100 MIME-Version: 1.0 Sent to CCL by: Jason Cole [cole|-|ccdc.cam.ac.uk] Many years ago I wrote a rather crude algorithm that detects symmetry in Molecules (it is published - see Acta Cryst. (2002). B58, 640-646) http://scripts.iucr.org/cgi-bin/paper?S0108768102006675 I would not make any claims to the algorithms robustness, but it did for what we wanted. Tolerances are tricky with this kind of thing: I don't think it would work for really big molecules. Since then, I have found out about some other publications: for example Algorithms for Unique and Unambiguous Coding and Symmetry Perception of Molecular Structure Diagram. I. Vector Function for Automorphism Partitioning J. Chem. Inf. Comput. Sci., 1980, 20 (2), pp 116-120 http://pubs.acs.org/doi/abs/10.1021/ci60022a013 I think, if we'd used his algorithm we'd have got better results probably (though it's a pretty stiff read!) - it say's Diagram in the title, but I believe, in principle, the approaches are extensible to 3D. Jason Cole > -----Original Message----- > From: owner-chemistry+cole==ccdc.cam.ac.uk..ccl.net [mailto:owner- > chemistry+cole==ccdc.cam.ac.uk..ccl.net] On Behalf Of Michel Petitjean > petitjean.chiral_+_gmail.com > Sent: 27 September 2012 08:04 > To: Jason Cole > Subject: CCL: Symmetry > > > Sent to CCL by: Michel Petitjean [petitjean.chiral]_[gmail.com] Dear Will, I did > some work in quasi-symmetry measurements (see my freeware QCM, URL > below). > I would be delighted to learn about the algorithm which "symmetrizes the > structure". > Can you give me the references ? > Thanks. > Michel. > > Michel Petitjean > MTi, INSERM UMR-S 973, University Paris 7, > 35 rue Helene Brion, 75205 Paris Cedex 13, France. > Phone: +331 5727 8434; Fax: +331 5727 8372 > E-mail: petitjean.chiral^_^gmail.com (preferred), michel.petitjean^_^univ- > paris-diderot.fr > http://petitjeanmichel.free.fr/itoweb.petitjean.html > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#QCM > > 2012/9/26 William F. Polik polik]-[hope.edu : > > ... > > > > WebMO (www.webmo.net) can identify the point group of any molecule, > > and also the subgroups. Furthermore, if the molecule is "nearly > > symmetric," it can identify the nearest point group and subgroups, and > then symmetrize the structure as requested. > > ...To > recover the email address of the author of the message, please change the > strange characters on the top line to the .. sign. You can also look up the X- > Original-From: line in the mail header.> LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmaster..ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. From owner-chemistry@ccl.net Thu Sep 27 14:18:00 2012 From: "Sergio Antonio Rodriguez drsergiorod]_[gmail.com" To: CCL Subject: CCL:G: help with a calculation Message-Id: <-47683-120927121853-1975-xjgjFhMcfDCqeif7H39hEg[]server.ccl.net> X-Original-From: "Sergio Antonio Rodriguez" Date: Thu, 27 Sep 2012 12:18:52 -0400 Sent to CCL by: "Sergio Antonio Rodriguez" [drsergiorod(!)gmail.com] Hi!! I need obtain the spin densities for a radical with Gaussian 03. How can obtained the spin densities values for each atom of the molecule? Thanks a lot!!! From owner-chemistry@ccl.net Thu Sep 27 19:48:00 2012 From: "Rajarshi Guha rajarshi.guha|,|gmail.com" To: CCL Subject: CCL: CINF Webinar: Practical cheminformatics workflows with mobile apps Message-Id: <-47684-120927170524-2105-P0tfpFlcF5gHJ4qX3JAB/g- -server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 27 Sep 2012 17:05:16 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha_._gmail.com] I'm pleased to announce that the ACS Division of Chemical Information will be hosting a series of free webinars on topics related to chemical information. The webinars will be open to everybody and our first speaker in this series will be Dr. Alex Clark, who'll be talking about cheminformatics workflows and mobile applications. More details below or at http://www.acscinf.org/about/news/20120918.php: Webinar: Practical cheminformatics workflows with mobile apps Date: October 3, 2012 Time: 11 am Eastern time (US) View the Webinar: http://acspubs2.adobeconnect.com/cinfwebinar-oct2012 Abstract: In recent years smartphones and tablets have attained sufficient power and sophistication to replace conventional desktop and laptop computers for many tasks. Chemistry software is late to the party, but rapidly catching up. This webinar will explore some of the cheminformatics functionality that can currently be performed using mobile apps. A number of workflow scenarios will be discussed, such as: creating and maintaining chemical data (molecules, reactions, numbers & text); searching chemical databases and utilising the results; structure-aware lab notebooks; visualisation and structure-activity analysis; property calculation using remote webservices; and a multitude of ways to share data collaboratively, and integrate modular apps within distributed and heterogeneous workflows. Speaker: Alex M. Clark graduated from the University of Auckland, New Zealand, with a Ph.D. in synthetic organometallic chemistry, then went on to work in computational chemistry. His chemistry background spans both the lab bench and development of software for a broad variety of 2D and 3D computer aided molecular design algorithms and user interfaces. He is the founder of Molecular Materials Informatics, Inc., which is dedicated to producing next-generation cheminformatics software for emerging platforms such as mobile devices and cloud computing environments. -- Rajarshi Guha | http://blog.rguha.net Chair, ACS Division of Chemical Information From owner-chemistry@ccl.net Thu Sep 27 20:27:00 2012 From: "=?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= segalemb*usp.br" To: CCL Subject: CCL:G: help with a calculation Message-Id: <-47685-120927202054-2434-+4ZjaptIjBvKQ6Z7i0CcvQ]_[server.ccl.net> X-Original-From: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 27 Sep 2012 21:20:44 -0300 Mime-Version: 1.0 (Mac OS X Mail 6.1 \(1498\)) Sent to CCL by: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= [segalemb#usp.br] Dear Sergio, If you do an unrestricted method (UHF, UDFT or UMP2) you will find the spin densities in the Mulliken population analysis, just after the Mulliken charges. Best regards, Sergio Em 27/09/2012, ās 13:18, Sergio Antonio Rodriguez drsergiorod]_[gmail.com escreveu: > > Sent to CCL by: "Sergio Antonio Rodriguez" [drsergiorod(!)gmail.com] > Hi!! I need obtain the spin densities for a radical with Gaussian 03. How can > obtained the spin densities values for each atom of the molecule? Thanks a > lot!!!> >