=A0

*************************************************
Dr. I= . SARAVANAN, M.Sc., M.Phil., PGDCA., PGDHRM., Ph.D.,
Consultant,

--f46d040838d31c25a404cb37f8b1-- From owner-chemistry@ccl.net Thu Oct 4 07:41:00 2012 From: "Sergio Manzetti sergio.manzetti]*[gmx.com" To: CCL Subject: CCL:G: Resonance energy Message-Id: <-47713-121004073514-17002-cpzOklGBIlSoH3KaWmOgiw|-|server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary93581349350505163550" Date: Thu, 04 Oct 2012 13:35:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti!=!gmx.com] --========GMXBoundary93581349350505163550 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Robert, I agree on that Truhlar (and Friedman) are central references on this. However, how can a program (like Gaussian for isntance) be used to apply their model for resonance? Amy's suggestion is quite interesting, and could be a way to get a glance of resonance for certain non-modifed PAHs for instance. Sergio ----- Original Message ----- > From: Robert W. Gora robert.gora===pwr.wroc.pl Sent: 10/04/12 10:01 AM To: Manzetti, Sergio Subject: CCL: Resonance energy Dear Amy, Dear All, > Maybe my thinking is too simplistic. It seems like you could calculate the > predicted value for the enthalpy of complete hydrogenation of your system > which would be N times (N=# double bonds) that of one double bond). Then > subtract the actual predicted value for the complete hydrogenation (which > will be less due to the resonance stabilization). That difference should be > the resonance energy of the system. I don't think what you propose to calculate constitutes the resonance stabilization energy even though the enthalpy of hydrogenation is obviously somehow related. Apart from the recent paper by Rashid et al. I have mentioned previously, I could recommend a discussion in the Journal of Chemical Education that originated from Robert C. Kerber's paper "If It’s Resonance, What Is Resonating?" [DOI 10.1021/ed083p223]. Personally, I am particularly fond of Donald G. Truhlar's reply "The Concept of Resonance" ibid [DOI 10.1021/ed084p781], which captures the essence of resonance as it is understood in the quantum chemistry community: "The meaning of resonance energy as it appears in valence bond theory is the lowering of the calculated ground state electronic energy when one improves a quantum mechanical model containing a single valence bond structure in the wave function to include other significant valence bond structures." Where the term structure corresponds to "a single set of spin orbitals with a spin coupling corresponding to a particular covalent or ionic bonding scheme." Best, Robert PS. By the way, I apologize Brian Salter-Duke for forgetting to mention his excellent code ;) -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora] [http://www.researcherid.com/rid/B-3919-2010] --========GMXBoundary93581349350505163550 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Robert, = I agree on that Truhlar (and Friedman) are central references on this. Howe= ver, how can a program (like Gaussian for isntance) be used to apply their = model for resonance?
=20 Amy's suggestion is quite interesting, and could be a way to get a glance o= f resonance for certain non-modifed PAHs for instance.
=20
=20 Sergio
=20
=20

=20 =C2=A0

=20

=20 ----- = Original Message -----

=20

=20 From: = Robert W. Gora robert.gora=3D=3D=3Dpwr.wroc.pl

=20

=20 Sent: = 10/04/12 10:01 AM

=20

=20 To: Ma= nzetti, Sergio

=20

=20 Subjec= t: CCL: Resonance energy

=20
=20

=20

=20
Dear Amy,=20
Dear All,=20

> Maybe my thinking is too simplistic. It seems like you could calculate=
 the=20
> predicted value for the enthalpy of complete hydrogenation of your sys=
tem=20
> which would be N times (N=3D# double bonds) that of one double bond). =
Then=20
> subtract the actual predicted value for the complete hydrogenation (wh=
ich=20
> will be less due to the resonance stabilization). That difference shou=
ld be=20
> the resonance energy of the system.=20

I don't think what you propose to calculate constitutes the resonance=20
stabilization energy even though the enthalpy of hydrogenation is obviously=
=20
somehow related.=20

Apart from the recent paper by Rashid et al. I have mentioned previously, I=
=20
could recommend a discussion in the Journal of Chemical Education that=20
originated from Robert C. Kerber's paper "If It=E2=80=99s Resonance, What I=
s=20
Resonating?" [DOI 10.1021/ed083p223].=20

Personally, I am particularly fond of Donald G. Truhlar's reply "The Concep=
t=20
of Resonance" ibid [DOI 10.1021/ed084p781], which captures the essence of=
=20
resonance as it is understood in the quantum chemistry community:=20

"The meaning of resonance energy as it appears in valence bond theory is th=
e=20
lowering of the calculated ground state electronic energy when one improves=
 a=20
quantum mechanical model containing a single valence bond structure in the=
=20
wave function to include other significant valence bond structures." Where =
the=20
term structure corresponds to "a single set of spin orbitals with a spin=20
coupling corresponding to a particular covalent or ionic bonding scheme."=
=20

Best,=20
Robert=20

PS. By the way, I apologize Brian Salter-Duke for forgetting to mention his=
=20
excellent code ;)=20

--=20
Robert W. G=C3=B3ra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.=
info]=20
[http://www.researchgate.net/profile/Robert_Gora]=20
[http://www.researcherid.com/rid/B-3919-2010]

=20

=20 =C2=A0

=20
=20 --========GMXBoundary93581349350505163550-- From owner-chemistry@ccl.net Thu Oct 4 08:16:01 2012 From: "Gkourmpis, Thomas Thomas.Gkourmpis##borealisgroup.com" To: CCL Subject: CCL:G: Polymer Construction Message-Id: <-47714-121004063255-31754-Y9hWNwgDdo39wiKgbKz+LQ a server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_1F6EE93266D93848A521EDB3F2B53E303553DFA4CMS02mignetwork_" Date: Thu, 4 Oct 2012 12:32:43 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis[A]borealisgroup.com] --_000_1F6EE93266D93848A521EDB3F2B53E303553DFA4CMS02mignetwork_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi=0D=0A=0D=0ARegarding the polymer in Gaussian the question is how many re= peating units you need=2E If you need only a few units and each is small yo= u can always construct it by hand in GaussView=2E If on the other hand you = want a "proper" chain with many units then you'll be better off if you use = any of the builders used in Molecular Dynamics packages and construct your = system there=2E Then you can convert it to any file that Gaussian can read = and use it as you see fit=2E=0D=0A=0D=0AHave I answered your question or I = misunderstood something?=0D=0A=0D=0AThomas=0D=0A=0D=0AFrom: owner-chemistry= +thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom:-:ccl=2Enet [mailto:owner-chemis= try+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom:-:ccl=2Enet] On Behalf Of Sha= ran sara180681%%gmail=2Ecom=0D=0ASent: Thursday, October 04, 2012 10:59 AM= =0D=0ATo: Gkourmpis, Thomas=0D=0ASubject: CCL:G: Polymer Construction=0D=0A= =0D=0AHi=0D=0A=0D=0ACan somebody help me in constructing Polymeric unit in = Gaussian for optimization=2E I am not clear on constructing the Translation= al vector for polymeric unit=2E I went through the example given in Gaussia= n 03, I am not clear on few fixed values supplied in the examples in constr= ucting the polymeric unit=2E=0D=0A=0D=0ASome helping hand will be greateful= =2E=2E thanks in advance=2E=0D=0A=0D=0AWith best regards=0D=0A=0D=0A*******= ******************************************=0D=0ADr=2E I=2E SARAVANAN, M=2ES= c=2E, M=2EPhil=2E, PGDCA=2E, PGDHRM=2E, Ph=2ED=2E,=0D=0AConsultant,=0D=0A= =0D=0A=0D=0AThis Email and any files transmitted with it are confidential a= nd=0D=0Aintended solely for the use of the individual or the entity to whom= =0D=0Ait is addressed=2E If you have received this Email by error, please= =0D=0Anotify the sender and delete the material from any storage device=2E= =0D=0ABorealis extends no warranties and makes no representations as to=0D= =0Athe accuracy or completeness of the information provided=2E It is the=0D= =0Acustomer's responsibility to inspect and test our products and=0D=0Atech= nical advice in order to satisfy itself as to the suitability=0D=0Aof the p= roducts and technical advice for the customer's particular=0D=0Apurpose=2E = --_000_1F6EE93266D93848A521EDB3F2B53E303553DFA4CMS02mignetwork_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi=

Regarding the polymer in Gaussian the question is how many rep= eating units you need=2E If you need only a few units and each is small you= can always construct it by hand in GaussView=2E If on the other hand you w= ant a “proper” chain with many units then you’ll be bette= r off if you use any of the builders used in Molecular Dynamics packages an= d construct your system there=2E Then you can convert it to any file that G= aussian can read and use it as you see fit=2E

Have I answe= red your question or I misunderstood something?

Thomas

From: owner-= chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom:-:ccl=2Enet [mailto:own= er-chemistry+thomas=2Egkourmpis=3D=3Dborealisgroup=2Ecom:-:ccl=2Enet] On B= ehalf Of Sharan sara180681%%gmail=2Ecom
Sent: Thursday, Octob= er 04, 2012 10:59 AM
To: Gkourmpis, Thomas
Subject: CCL= :G: Polymer Construction

<= p class=3DMsoNormal>

Ca= n somebody help me in constructing Polymeric unit in Gaussian for optimizat= ion=2E I am not clear on constructing the Translational vector for polymeri= c unit=2E I went through the example given in Gaussian 03, I am not cl= ear on few fixed values supplied in the examples in constructing the polyme= ric unit=2E

Some helping hand will be greateful=2E= =2E thanks in advance=2E

&nbs= p;

With best regards

*************************************************
Dr=2E I=2E SARAVANAN, M=2ESc=2E, M=2EPhil=2E, PGDCA= =2E, PGDHRM=2E, Ph=2ED=2E,
Consultant,

=0D=0AThis Email and any files transm= itted with it are confidential and intended solely for the use of the indiv= idual or the entity to whom it is addressed=2E If you have received this Em= ail by error, please notify the sender and delete the material from any sto= rage device=2E Borealis extends no warranties and makes no representations = as to the accuracy or completeness of the information provided=2E It is the= customer's responsibility to inspect and test our products and technical a= dvice in order to satisfy itself as to the suitability of the products and = technical advice for the customer's particular purpose=2E --_000_1F6EE93266D93848A521EDB3F2B53E303553DFA4CMS02mignetwork_-- From owner-chemistry@ccl.net Thu Oct 4 09:31:00 2012 From: "Robert W. Gora robert.gora ~~ pwr.wroc.pl" To: CCL Subject: CCL:G: [CCL] Resonance energy Message-Id: <-47715-121004092005-24145-ht0dyurEnJR2VyPJHQunJw]^[server.ccl.net> X-Original-From: "Robert W. Gora" Content-id: Content-type: multipart/mixed; boundary="Boundary_(ID_vAHn+k5dgOsxFW9C+r7DOA)" Date: Thu, 04 Oct 2012 15:19:58 +0200 (CEST) MIME-version: 1.0 Sent to CCL by: "Robert W. Gora" [robert.gora(!)pwr.wroc.pl] This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. --Boundary_(ID_vAHn+k5dgOsxFW9C+r7DOA) Content-id: Content-type: TEXT/PLAIN; CHARSET=utf-8; FORMAT=flowed Content-transfer-encoding: 8BIT Sergio, > Robert, I agree on that Truhlar (and Friedman) are central references on > this. However, how can a program (like Gaussian for isntance) be used to > apply their model for resonance? Well, if you insist on using Gaussian then there is a method called generalized valence-bond GVB but this is really a particular type of MCSCF and I do not think it would be usefull if you are really interested in resonance stabilization. I believe that you need a vb wavefunction for that and Brian has provided references to pretty much every possibilities. My personal preference is CASVB implemented in MOLCAS and MOLPRO, but the resonance stabilization could be extracted from any of the VB codes. In general, and oversimplifying VB is like CI but in AO basis. At some point you need to select a set of structures, which correspond to particular modes of spin coupling. If you subtract the energy of a single valence structure > from that of a full VB (within a chosen approximation), you will end up with a resonance stabilization. This is particularly easy in CASVB or SCVB implemented in VB2000 (the two methods are in fact equivalent). Have a look for instance at Grant Hill's paper in JPCA [doi:10.1021/jp057458d] for the details how this could be done for benzene-like molecules. I can sent you an input file for molcas and/or molpro if you are interested. > Amy's suggestion is quite interesting, and could be a way to get a glance of > resonance for certain non-modifed PAHs for instance. Sure, but also a bit more than that (I mean not only the resonance) :) Cheers, Robert -- Robert W. Góra, Theoretical Chemistry Group, ICHFiT, WUT [http://zcht.info] [http://www.researchgate.net/profile/Robert_Gora] [http://www.researcherid.com/rid/B-3919-2010] --Boundary_(ID_vAHn+k5dgOsxFW9C+r7DOA)-- From owner-chemistry@ccl.net Thu Oct 4 10:48:00 2012 From: "Andrew Voronkov drugdesign~~yandex.ru" To: CCL Subject: CCL: question about software for synthetic accessibility evaluation and design of synthetic routes Message-Id: <-47716-121003101042-14829-G9De3jDuegmxgWKl6f1fqQ[]server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: base64 Content-Type: text/html; charset=utf-8 Date: Wed, 03 Oct 2012 18:10:28 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign*o*yandex.ru] PGRpdj5EZWFyIFdvbGYsIFRIRVJFU0EgaXMgdW5mb3J1bmF0ZWx5IGlzIGRpc2NvbnRpbnVlZCBi eSBNb2xlY3VsYXIgTmV0d29ya3MgYW5kIHRoZXkgZG9uJ3Qgc2F5IGJ5IHdoaWNoIHJlYXNvbiBh bmQgZG9uJ3Qgd2FudCB0byBwcm92aWRlIGl0LjwvZGl2PjxkaXY+RG8geW91IGtub3cgaWYgdGhl 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12:10:00 2012 From: "Rachelle Bienstock biensto1===niehs.nih.gov" To: CCL Subject: CCL: Programs for dsigning synthesis Message-Id: <-47717-121004120846-904-2Fsauh+3JhF8rsUR7G7rPA(-)server.ccl.net> X-Original-From: "Rachelle Bienstock" Date: Thu, 4 Oct 2012 12:08:45 -0400 Sent to CCL by: "Rachelle Bienstock" [biensto1%a%niehs.nih.gov] I do not work for any of these commercial companies and am not endorsing or advertising their products. This is just informational for the people who asked about software that suggests accessibility and design of chemical synthetic routes. SimBioSys (http://www.simbiosys.com) has products ArChem and CAESA which computationally suggest chemical compound synthetic routes. Elsevier has Reaxys (https://www.reaxys.com/info/about-overview). I hope this information is helpful. I am not aware of free and/or open source products, but they might exist as well. From owner-chemistry@ccl.net Thu Oct 4 14:07:01 2012 From: "Victor Rosas Garcia rosas.victor,,gmail.com" To: CCL Subject: CCL: question about software for synthetic accessibility evaluation and design of synthetic routes Message-Id: <-47718-121004122318-6512-n/neTkqthkc5jxkRZn0YuQ.@.server.ccl.net> X-Original-From: Victor Rosas Garcia Content-Type: multipart/alternative; boundary=0015174a0e5cc01afe04cb3e2b2a Date: Thu, 4 Oct 2012 11:23:09 -0500 MIME-Version: 1.0 Sent to CCL by: Victor Rosas Garcia [rosas.victor###gmail.com] --0015174a0e5cc01afe04cb3e2b2a Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Andrew, just found this: Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation James Law, Zsolt Zsoldos, Aniko Simon, Darryl Reid, Yang Liu, Sing Yoong Khew, A. Peter Johnson, Sarah Major, Robert A. Wade, and Howard Y. Ando J. Chem. Inf. Model., 2009, 49 (3), 593-602=95 DOI: 10.1021/ci800228y it might be of interest Victor 2012/10/3 Andrew Voronkov drugdesign~~yandex.ru > Dear Wolf, THERESA is unforunately is discontinued by Molecular Networks > and they don't say by which reason and don't want to provide it. > Do you know if there are any other analogs of it? > I don't know what is the reason to discontinue such interesting and usefu= l > program. Even if it is not accurate this can be always checked by organic > chemist and anyway...almost all software programs are provided without an= y > warrant. So if anyone else knows similar programs, or has old version of > Theresa, please let me know. > They have now software, called Sylvia, which also looks very interesting > and I want to evaluate it, but it doesn't suggest synthetic routes > unfortunately. > > Best regards, > Andrew > > 12.09.2012, 00:47, "Wolf Ihlenfeldt wdi|*|xemistry.com" < > owner-chemistry]~[ccl.net>: > > > THERESA, by Molecular Networks (www.mol-net.de) > > > On Tue, Sep 11, 2012 at 9:03 AM, Andrew Voronkov drugdesign.~!~.yandex.ru > wrote: > > > Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru] > Dear CCL users, > can you please, recommend some software, which is able to evaluate > synthetic accessibility of specified newly designed molecules and which = is > able to suggest synthesis routes for those, which are synthesizable? > > > Best regards, > Andrew > > > > -=3D This is automatically added to each message by the mailing script = =3D- > E-mail to subscribers: CHEMISTRY~!~ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST~!~ccl.net or use> > > > > -- > Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi~!~xemistry.com > Phone: +49 6174 201455 - Fax +49 6174 209665 > --- > xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenf= eldt > Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany > HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > > --0015174a0e5cc01afe04cb3e2b2a Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Andrew,

just found this:

Route Designer: A Retrosyntheti= c Analysis Tool Utilizing Automated Retrosynthetic Rule Generation
James= Law, Zsolt Zsoldos, Aniko Simon, Darryl Reid, Yang Liu, Sing Yoong
Khew= , A. Peter Johnson, Sarah Major, Robert A. Wade, and Howard Y. Ando
J. Chem. Inf. Model., 2009, 49 (3), 593-602=95 DOI: 10.1021/ci800228y
it might be of interest

Victor

2= 012/10/3 Andrew Voronkov drugdesign~~yandex.ru= <owner-chemistry]~[ccl.net>

Dear Wolf, THERESA is unforunately is d= iscontinued by Molecular Networks and they don't say by which reason an= d don't want to provide it.

Do you know if there are any other analogs of it?
I don'= t know what is the reason to discontinue such interesting and useful progra= m. Even if it is not accurate this can be always checked by organic chemist= and anyway...almost all software programs are provided without any warrant= . So if anyone else knows similar programs, or has old version of Theresa, = please let me know.

They have now software, called Sylvia, which also looks very interesti= ng and I want to evaluate it, but it doesn't suggest synthetic routes u= nfortunately.
=A0
Best regards,
Andrew

=A0
12.09.2012, 00:47, "Wolf Ihlenfeldt wdi|*|xemistry.com" <owner-chemistry]~[ccl= .net>:

THERESA, by Molecular Networks (www.mol-net.de)

On Tue, Sep 11, 2012 at 9:03 AM, Andrew Voronkov drugdesign.~!~.yandex.ru <<= a href=3D"mailto:owner-chemistry~!~ccl.net" target=3D"_blank">owner-chemist= ry~!~ccl.net> wrote:

Sent to CCL by: Andrew Voronkov [drugdesign**yandex.ru]
Dear CCL users,
can= you please, recommend some software, which is able to evaluate synthetic a= ccessibility of =A0specified newly designed molecules and which is able to = suggest synthesis routes for those, which are synthesizable?

Best regards,
Andrew

-=3D This is automat= ically added to each message by the mailing script =3D-
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--
Wolf-D. Ihlenfeldt -=A0 Xemistry GmbH - wdi~!~xemistry.com
Phone: +49 6174= 201455 - Fax +49 6174 209665
---
xemistry gmbh = =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany
HR K=F6nigstein = B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719=