Dear Elham,

Please do remember that what you = call double, triple bond etc. has no meaning in the context of ab initio or= DFT (also within the context of semi-empirical theory!)! If you see the in= put file of your software, you will find NO information regarding the "bond= s"!

Forget about bonds and submit your job!

Good luck,

Cina

*********************************************= ********************************************

Cina Fo= routan-Nejad, Ph. D.

School of Chemistry, College of= Science,

University of Tehran, Tehran, Iran

http://independent.academia.edu/CinaForoutanNe= jad

From: E= lham Abdolhamidi flight.66.ab---gmail.com <owner-chemistry++ccl.net> To: "Foroutan-Nejad, Ci= na " <canyslopus++yahoo.co.uk>
Sent: Wednesday, 9 May 2012, 11:32
Subject: CCL: question on Gaussview
=

Sent to CCL by: "Elham Abdolhamidi" [flight.6= 6.ab~~gmail.com]
I have been working with gaussview (g09) and I have som= e problems in drawing polymers. You know, I draw the monomer and then I use PBC to make = the polymer. but after combining in PBC , there appears some singlet, doubl= et and triplet bonds (which are not correct and they should not be there!).=
I have also read different manuals for gaussview but I still have this= problem and I cannot get a good structure for the polymers.
I'll be so = thankful if you help me solving this problem.
Elham

-=3D = This is automatically added to each message by the mailing script =3D-
T= o recover the email address of the author of the message, please change
=
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---1952966989-1677414893-1336567037=:81123-- From owner-chemistry@ccl.net Wed May 9 10:28:00 2012 From: "Christopher Baker bmcmutations++gmail.com" To: CCL Subject: CCL: Mutation: Annotation, Interpretation and Management of (AIMM2012) Message-Id: <-46873-120509080742-12539-f/1wLbKI6HNCQJSswNteEQ%a%server.ccl.net> X-Original-From: Christopher Baker Content-Type: multipart/alternative; boundary=f46d04428c9c44c91c04bf9959cc Date: Wed, 9 May 2012 09:07:35 -0300 MIME-Version: 1.0 Sent to CCL by: Christopher Baker [bmcmutations]_[gmail.com] --f46d04428c9c44c91c04bf9959cc Content-Type: text/plain; charset=ISO-8859-1 *AIMM 2012 - CALL FOR PAPERS* Annotation, Interpretation and Management of Mutations (AIMM2012), a workshop at the European Conference on Computational Biology (ECCB12) Sept 9th 2012, Basel, Switzerland. http://www.eccb12.org/workshops#ws2 http://www.unbsj.ca/sase/csas/data/aimm2012/ *Keynote Speaker* - Mauno Vihinen PhD, Professor of Medical Structural Biology (Lund). VARIATION ONTOLOGY: ontology for standardized, systematic description of effects and consequences of variations. *Important Dates* Abstract submission June 15 2012 Full paper submission July 1 2012 Acceptance notification July 30 2012 Final manuscript Aug 15 2012 AIMM2012 Workshop Sept 9 2012 *Workshop Themes* * Mutation Nomenclature, Databases and Metadata: Design, Content, Accuracy. * Mutation Data Integration, Phenotype Ontologies, Semantic Services and Reuse. * Semantic Integration and Interpretation of data linked to mutations and diseases * Impacts of Mutations: Prediction and Bootstrapping. * Extraction and grounding of mutations and impact annotations > from scientific literature * System Evaluations and Benchmarking http://www.unbsj.ca/sase/csas/data/aimm2012/themes.html http://www.unbsj.ca/sase/csas/data/aimm2010/themes.html http://www.ebi.ac.uk/Rebholz-srv/aimm.html *Submissions* We invite workshop papers (3000 words / 8 pages) and demonstrations. Early Abstracts should be no more than 500 words. Manuscripts should be focused around a specific challenge with a biomedical context where they suggest a solution, demonstrate feasibility and possibly also a meaningful evaluation. Pre-submission enquiries and variations to the deadlines above may be made in consultation with the Chris Baker bakerc=unb.ca * Author instructions can be obtained by sending an email to bmcmutations=gmail.com an automated reply will be sent and complete submissions should be uploaded to Easychair:https://www.easychair.org/conferences/?conf=aimm2012 *Journal Special Issue* A special issue in a biomedical scientific journal will be produced of the best contributions to the Workshop Proceedings. Papers have to address genuine themes relevant to the: Annotation, Interpretation and Management of Mutations (see below)* * Workshop Organizers / Special Issue Editors* - Christopher J. O. Baker - University of New Brunswick, Canada - Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, UK --f46d04428c9c44c91c04bf9959cc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable *AIMM 2012 - CALL FOR PAPERS*

Annotation, Interpretation and Management of Mutations (AIMM2012), a
workshop at the European Conference on Computational Biology (ECCB12)
Sept 9th 2012, Basel, Switzerland.
http://ww= w.eccb12.org/workshops#ws2
= http://www.unbsj.ca/sase/csas/data/aimm2012/

*Keynote Speaker*
- Mauno Vihinen PhD, Professor of Medical Structural Biology (Lund).
VARIATION ONTOLOGY: ontology for standardized, systematic description
of effects and consequences of variations.

*Important Dates*
Abstract submission =A0 =A0 =A0 June 15 2012
Full paper submission =A0 =A0 July 1 2012
Acceptance notification =A0 July 30 2012
Final manuscript =A0 =A0 =A0 =A0 =A0 =A0 Aug 15 2012
AIMM2012 Workshop =A0 =A0 =A0Sept 9 2012

*Workshop Themes*

=A0 * Mutation Nomenclature, Databases and Metadata: Design, Content, Accu= racy.
=A0 * Mutation Data Integration, Phenotype Ontologies, Semantic
Services and Reuse.
=A0 * Semantic Integration and Interpretation of data linked to
mutations and diseases
=A0 * Impacts of Mutations: Prediction and Bootstrapping.
=A0 * Extraction and grounding of mutations and impact annotations
> from scientific literature
=A0 * System Evaluations and Benchmarking

http://www.unbsj.ca/sase/csas/data/aimm2012/themes.html
http://www.unbsj.ca/sase/csas/data/aimm2010/themes.html
ht= tp://www.ebi.ac.uk/Rebholz-srv/aimm.html

*Submissions*

We invite workshop papers (3000 words / 8 pages) and demonstrations.
Early Abstracts should be no more than 500 words. Manuscripts should
be focused around a specific challenge with a biomedical context where
they suggest a solution, demonstrate feasibility and possibly also a
meaningful evaluation.

Pre-submission enquiries and variations to the deadlines above may be
made in consultation with the Chris Baker bakerc=unb.ca

=A0* Author instructions can be obtained by sending an email to
bmcmutations=gm= ail.com an automated reply =A0will be sent and complete
submissions should be uploaded to
=A0Easychair:https://www.easychair.org/conferences/?conf=3Daimm20= 12

*Journal Special Issue*

A special issue in a biomedical scientific journal will be produced of
the best contributions to the Workshop Proceedings. Papers have to
address genuine themes relevant to the: Annotation, Interpretation and
Management of Mutations (see below)*

* Workshop Organizers / Special Issue Editors*

- =A0Christopher J. O. Baker - University of New Brunswick, Canada
- =A0Dietrich Rebholz-Schuhmann, European Bioinformatics Institute, UK --f46d04428c9c44c91c04bf9959cc-- From owner-chemistry@ccl.net Wed May 9 11:54:00 2012 From: "Joe Golab joseph.golab .. ineos.com" To: CCL Subject: CCL: IR Spectra (Frequency Calculation) Message-Id: <-46874-120509115225-9158-BXf4oXJGMLJqud5nvITAFA**server.ccl.net> X-Original-From: "Joe Golab" Date: Wed, 9 May 2012 11:52:22 -0400 Sent to CCL by: "Joe Golab" [joseph.golab(-)ineos.com] CCL Members: We would like to study the IR spectrum of a molecule as a function of its conformation. Obviously, a strictly theoretical treatment can only predict one conformer's spectrum, i.e. the lowest energy one. But what if the environment around a molecule prevented it from existing in its "lowest energy" (geometry optimized) configuration? We cannot take the environment into account, i.e. use the environment to "force" conformations for the frequency calculation. So, is it possible to study the IR spectrum of a molecule as a function of its conformation? Thanks for your consideration. Joe ___________________________ Joseph T. Golab, PhD Molecular Modeling & Simulation Scientist Senior Research Scientist INEOS Technologies, Nitriles R&D Phone: +1 (630) 420-5063 Cell: +1 (630) 336-0063 Email: Joseph.Golab_at_ineos.com From owner-chemistry@ccl.net Wed May 9 12:30:00 2012 From: "dipankar roy theodip---gmail.com" To: CCL Subject: CCL: IR Spectra (Frequency Calculation) Message-Id: <-46875-120509122821-17020-WqZzB7pbKs/mARKt/9zl/A:_:server.ccl.net> X-Original-From: dipankar roy Content-Type: multipart/alternative; boundary=0015175cfbb04b320404bf9cfd96 Date: Wed, 9 May 2012 12:28:12 -0400 MIME-Version: 1.0 Sent to CCL by: dipankar roy [theodip__gmail.com] --0015175cfbb04b320404bf9cfd96 Content-Type: text/plain; charset=ISO-8859-1 Hi, You can optimize structures of different conformers and then calculate force constants and IR-frequencies (after making sure those conformers are minima). Regarding the environment of the around a molecule, if it is due to solvent effect, you can incorporate it in your calculation (so is for intramolecular interactions between molecules). Best, Dipankar Roy ----------------------------------- Dipankar Roy Brooklyn College Department of Chemistry 2900 Bedford Avenue Brooklyn, NY 11210 ----------------------------------- On Wed, May 9, 2012 at 11:52 AM, Joe Golab joseph.golab .. ineos.com < owner-chemistry(!)ccl.net> wrote: > > Sent to CCL by: "Joe Golab" [joseph.golab(-)ineos.com] > CCL Members: > > We would like to study the IR spectrum of a molecule as a function of its > conformation. > > Obviously, a strictly theoretical treatment can only predict one > conformer's spectrum, i.e. the lowest energy one. > > But what if the environment around a molecule prevented it from existing > in its "lowest energy" (geometry optimized) configuration? > > We cannot take the environment into account, i.e. use the environment to > "force" conformations for the frequency calculation. > > So, is it possible to study the IR spectrum of a molecule as a function of > its conformation? > > Thanks for your consideration. > > Joe > ___________________________ > Joseph T. Golab, PhD > Molecular Modeling & Simulation Scientist > Senior Research Scientist > INEOS Technologies, Nitriles R&D > Phone: +1 (630) 420-5063 > Cell: +1 (630) 336-0063 > Email: Joseph.Golab_at_ineos.com> > > -- ----------------------------------- Dr. Dipankar Roy Research Associate Brooklyn College Department of Chemistry 2900 Bedford Avenue Brooklyn, NY 11210 ----------------------------------- --0015175cfbb04b320404bf9cfd96 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

You can optimize structures of different conformers and then calcul= ate force constants and IR-frequencies (after making sure those conformers = are minima).

Regarding the environment of the around a molecule, = if it is due to solvent effect, you can incorporate it in your calculation = (so is for intramolecular interactions between molecules).

Best,

Dipankar Roy

-= ----------------------------------

Dipankar Roy

Brooklyn Coll= ege=A0
Department of Chemistry
2900 Bedford Avenue
Brooklyn, NY 11= 210

-----------------------------------

=A0

On Wed, May 9, 2012 at 11:52 AM, Joe Golab joseph.golab= .. ineos.com <owner-chemistry(!)ccl.= net> wrote:

Sent to CCL by: "Joe =A0Golab" [joseph.golab(-)ineos.com]
CCL Members:

We would like to study the IR spectrum of a molecule as a function of its c= onformation.

Obviously, a strictly theoretical treatment can only predict one conformer&= #39;s spectrum, i.e. the lowest energy one.

But what if the environment around a molecule prevented it from existing in= its "lowest energy" (geometry optimized) configuration?

We cannot take the environment into account, i.e. use the environment to &q= uot;force" conformations for the frequency calculation.

So, is it possible to study the IR spectrum of a molecule as a function of = its conformation?

Thanks for your consideration.

Joe
___________________________
Joseph T. Golab, PhD
Molecular Modeling & Simulation Scientist
Senior Research Scientist
INEOS Technologies, Nitriles R&D
Phone: += 1 (630) 420-5063
Cell: =A0+1 (630) 336-0063
Email: Josep= h.Golab_at_ineos.com

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(!)ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST(!)ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

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

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=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

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--
------------= -----------------------

Dr. Dipankar Roy

Research AssociateBrooklyn College
Department of Chemistry
2900 Bedford Avenue
Brooklyn, NY 11210

---------------= --------------------

--0015175cfbb04b320404bf9cfd96-- From owner-chemistry@ccl.net Wed May 9 13:16:00 2012 From: "carlos franca carfranca120[*]gmail.com" To: CCL Subject: CCL: IR Spectra (Frequency Calculation) Message-Id: <-46876-120509131351-7460-SUS4YwTzjYDAT42n+ksySQ\a/server.ccl.net> X-Original-From: carlos franca Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 09 May 2012 14:13:32 -0300 MIME-Version: 1.0 Sent to CCL by: carlos franca [carfranca120*gmail.com] Dear Joe Golab you can not take into account the environment of a molecule with ir calculation you can consider it in the optimization (eg using solvent effect) or using an experimental geometry (nmr or x-ray) if you do an optimization you will have several conformations wich can be available at room temperature you can calculate vibrational properties of these and to do a statistical average of those conformations best regards El 09/05/12 12:52, Joe Golab joseph.golab .. ineos.com escribi�: > Sent to CCL by: "Joe Golab" [joseph.golab(-)ineos.com] > CCL Members: > > We would like to study the IR spectrum of a molecule as a function of its conformation. > > Obviously, a strictly theoretical treatment can only predict one conformer's spectrum, i.e. the lowest energy one. > > But what if the environment around a molecule prevented it from existing in its "lowest energy" (geometry optimized) configuration? > > We cannot take the environment into account, i.e. use the environment to "force" conformations for the frequency calculation. > > So, is it possible to study the IR spectrum of a molecule as a function of its conformation? > > Thanks for your consideration. > > Joe > ___________________________ > Joseph T. Golab, PhD > Molecular Modeling& Simulation Scientist > Senior Research Scientist > INEOS Technologies, Nitriles R&D > Phone: +1 (630) 420-5063 > Cell: +1 (630) 336-0063 > Email: Joseph.Golab_at_ineos.com> > > From owner-chemistry@ccl.net Wed May 9 13:51:01 2012 From: "Arindam Ganguly arindamganguly]~[gmail.com" To: CCL Subject: CCL: IR Spectra (Frequency Calculation) Message-Id: <-46877-120509133513-17528-7zxWW4preL+cmKa36ykqBw : server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary=14dae9d2f66c734a0404bf9dec4c Date: Wed, 9 May 2012 13:35:04 -0400 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly-$-gmail.com] --14dae9d2f66c734a0404bf9dec4c Content-Type: text/plain; charset=ISO-8859-1 Hi Joe, I agree with Dipankar's assessment, in fact what you're suggesting is quite repeatedly done for molecules in gas phase, please refer to the paper for the same http://pubs.acs.org/doi/abs/10.1021/jp902521e. For small molecules you've take into consideration their symmetry of conformation, since that will decide the IR/Raman active modes. Thus, you could perform two sets of calculations one with solvent and without solvent, effectively reducing/removing the symmetry requirements. I hope this helps and let me know if you have any further questions on the paper. Thank you. Sincerely, Arindam On Wed, May 9, 2012 at 12:28 PM, dipankar roy theodip---gmail.com < owner-chemistry-.-ccl.net> wrote: > Hi, > You can optimize structures of different conformers and then calculate > force constants and IR-frequencies (after making sure those conformers are > minima). > Regarding the environment of the around a molecule, if it is due to > solvent effect, you can incorporate it in your calculation (so is for > intramolecular interactions between molecules). > > Best, > Dipankar Roy > > ----------------------------------- > Dipankar Roy > Brooklyn College > Department of Chemistry > 2900 Bedford Avenue > Brooklyn, NY 11210 > ----------------------------------- > > > On Wed, May 9, 2012 at 11:52 AM, Joe Golab joseph.golab .. ineos.com < > owner-chemistry^_^ccl.net> wrote: > >> >> Sent to CCL by: "Joe Golab" [joseph.golab(-)ineos.com] >> CCL Members: >> >> We would like to study the IR spectrum of a molecule as a function of its >> conformation. >> >> Obviously, a strictly theoretical treatment can only predict one >> conformer's spectrum, i.e. the lowest energy one. >> >> But what if the environment around a molecule prevented it from existing >> in its "lowest energy" (geometry optimized) configuration? >> >> We cannot take the environment into account, i.e. use the environment to >> "force" conformations for the frequency calculation. >> >> So, is it possible to study the IR spectrum of a molecule as a function >> of its conformation? >> >> Thanks for your consideration. >> >> Joe >> ___________________________ >> Joseph T. Golab, PhD >> Molecular Modeling & Simulation Scientist >> Senior Research Scientist >> INEOS Technologies, Nitriles R&D >> Phone: +1 (630) 420-5063 >> Cell: +1 (630) 336-0063 >> Email: Joseph.Golab_at_ineos.com** >> E-mail to subscribers: CHEMISTRY^_^ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST^_^ccl.net or use>> **>> >> >> > > > -- > ----------------------------------- > Dr. Dipankar Roy > Research Associate > Brooklyn College > Department of Chemistry > 2900 Bedford Avenue > Brooklyn, NY 11210 > ----------------------------------- > > -- Arindam Ganguly, Ph.D. Scientist, USP Applied Compendial Research-Spectrometry Laboratory http://www.linkedin.com/in/arindamganguly --14dae9d2f66c734a0404bf9dec4c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Joe,

I agree with Dipankar's assessment, in fact what you're= suggesting is quite repeatedly done for molecules in gas phase, please ref= er to the paper for the same=A0http://pubs.acs.org/doi/abs/10.1021/jp902521e.=A0

For small molecules you've take into=A0consideratio= n their symmetry of conformation, since that will decide the IR/Raman activ= e modes.=A0=A0Thus, you could perform two sets of calculations one with sol= vent and without solvent, effectively reducing/removing the symmetry=A0requ= irements. I hope this helps and let me know if you have any further questio= ns on the paper. Thank you.

Sincerely,
Arindam

On Wed, May 9, 2012 at 12:28 PM, dipankar roy theodip---gmail.com <owner-chemistry-.-ccl.net><= /span> wrote:

Hi,
You can optimize structures of diffe= rent conformers and then calculate force constants and IR-frequencies (afte= r making sure those conformers are minima).

Regarding the environment of the around a molecule, if it is due to so= lvent effect, you can incorporate it in your calculation (so is for intramo= lecular interactions between molecules).

Best,
Dipankar Roy

-= ----------------------------------
Dipankar Roy
Brooklyn Coll= ege=A0
Department of Chemistry
2900 Bedford Avenue
Brooklyn, NY 11= 210

-----------------------------------
=A0

On Wed, May 9, 2012 at 11:52 AM, Joe = Golab joseph.golab .. ineos.= com <owner-chemistry^_^ccl.net> wrote:

Sent to CCL by: "Joe =A0Golab" [joseph.golab(-)ineos.com]
CCL Members:

We would like to study the IR spectrum of a molecule as a function of its c= onformation.

Obviously, a strictly theoretical treatment can only predict one conformer&= #39;s spectrum, i.e. the lowest energy one.

But what if the environment around a molecule prevented it from existing in= its "lowest energy" (geometry optimized) configuration?

We cannot take the environment into account, i.e. use the environment to &q= uot;force" conformations for the frequency calculation.

So, is it possible to study the IR spectrum of a molecule as a function of = its conformation?

Thanks for your consideration.

Joe
___________________________
Joseph T. Golab, PhD
Molecular Modeling & Simulation Scientist
Senior Research Scientist
INEOS Technologies, Nitriles R&D
Phone: +1 (630) 420-5063
Cell: =A0+1 (630) 336-0063
Email: Josep= h.Golab_at_ineos.com

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY^_^ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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

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Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

=A0 =A0 =A0 h= ttp://www.ccl.net/spammers.txt

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--
----------------------------------= -
Dr. Dipankar Roy
Research Associate
Brooklyn College Department of Chemistry
2900 Bedford Avenue
Brooklyn, NY 11210
---------------= --------------------

Arindam G= anguly, Ph.D.
Scientist, USP
Applied Compendial Research-Spectrometry= Laboratory
http://www.linkedin.com/in/arindamganguly

--14dae9d2f66c734a0404bf9dec4c--