From owner-chemistry@ccl.net Thu May 10 00:45:01 2012 From: "Sharan sara180681%%gmail.com" To: CCL Subject: CCL: question on Gaussview Message-Id: <-46878-120510004244-31375-P8kL3WMZvVRsvCjv3vv8LA%server.ccl.net> X-Original-From: Sharan Content-Type: multipart/alternative; boundary=e89a8f2350979dac3d04bfa73ff8 Date: Thu, 10 May 2012 10:12:34 +0530 MIME-Version: 1.0 Sent to CCL by: Sharan [sara180681*gmail.com] --e89a8f2350979dac3d04bfa73ff8 Content-Type: text/plain; charset=ISO-8859-1 Dear Elham yes i agree Cina that in case of abinitio evethough you draw the structure as single and double bonds, program translates that into actual bond lengths. After optimization optimization, you will end up with exact bond lengths from which one can interpret whether is there a bond length. i have question for you i was also trying to construct polymers but with the example given in guassian help its not clear for me how to construct it using PBC because there are manually enter values what are they? If you have any insight please help me out Wtih regards Dr. Saravanan On Wed, May 9, 2012 at 6:07 PM, cina foroutan canyslopus|-|yahoo.co.uk < owner-chemistry*o*ccl.net> wrote: > 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 input file of your software, you > will find NO information regarding the "bonds"! > Forget about bonds and submit your job! > > Good luck, > Cina > > ***************************************************************************************** > Cina Foroutan-Nejad, Ph. D. > School of Chemistry, College of Science, > University of Tehran, Tehran, Iran > http://independent.academia.edu/CinaForoutanNejad > > > > > ________________________________ > From: Elham Abdolhamidi flight.66.ab---gmail.com ccl.net> > To: "Foroutan-Nejad, Cina " > Sent: Wednesday, 9 May 2012, 11:32 > Subject: CCL: question on Gaussview > > > Sent to CCL by: "Elham Abdolhamidi" [flight.66.ab~~gmail.com] > I have been working with gaussview (g09) and I have some 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, > doublet 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> the strange characters on the top line to the |,| sign. You can also> > E-mail to administrators: CHEMISTRY-REQUEST|,|ccl.net or use> > > ---1952966989-1677414893-1336567037:81123 > Content-Type: text/html; charsetiso-8859-1 > Content-Transfer-Encoding: quoted-printable > >
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 input file of your software, you will find NO > information regarding the "bonds"!
Forget about > bonds and submit your > job!

Good > luck,
Cina
*****************************************************************************************
Cina > Foroutan-Nejad, Ph. D.
School of Chemistry, College > of Science,
University of Tehran, Tehran, > Iran
> http://independent.academia.edu/CinaForoutanNejad



>
>
size="1"> From: Elham > Abdolhamidi flight.66.ab---gmail.com <owner-chemistry|,|ccl.net>
> To: "Foroutan-Nejad, Cina " > <canyslopus|,|yahoo.co.uk>
Sent: Wednesday, 9 May 2012, 11:32
style="font-weight: bold;">Subject: CCL: question on > Gaussview


Sent to CCL by: "Elham  > Abdolhamidi" [flight.66.ab~~gmail.com]
I have been working with > gaussview (g09) and I have some 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, > doublet 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



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-- ************************************************** Dr. I. SARAVANAN, M.Sc., M.Phil., PGDCA., PGDHRM., Ph.D., Consultant, **PerkinElmer Informatics,* UVJ Technologies Pvt.Ltd, 3rd Floor ,Plot No. 16 A, Cochin Special Economic Zone (CSEZ) Seaport Airport Road, Kakkanad, Cochin - 682 037 Kerala ************************************************** Res: No. 10, Neithal street, Solainagar, Muthialpet, Puducherry - 605 003 Cell: 9895079171 ************************************************** --e89a8f2350979dac3d04bfa73ff8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Elham
=A0
yes i agree Cina that in case of ab= initio evethough you draw the structure as single and double bonds, program= translates that into actual bond lengths. After optimization optimization,= you will end up with exact bond lengths from which one can interpret wheth= er is there a bond length.
=A0
i have question for you i was also trying to construct p= olymers but with the example given in guassian help its not clear for me ho= w to construct it using PBC because there are manually enter values what ar= e they? If you have any insight please help me out
=A0
=A0
Wtih regards
=A0
Dr. S= aravanan

On Wed, May 9, 2012 at 6:0= 7 PM, cina foroutan canyslopus|-|yahoo.co.uk= <owner-chemistry*o*ccl.net> wrote:
Dear Elham,

Please do remember that what you call double, triple bond etc. has no meani= ng in the context of ab initio or DFT (also within the context of semi-empi= rical theory!)! If you see the input file of your software, you will find N= O information regarding the "bonds"!
Forget about bonds and submit your job!

Good luck,
Cina
***************************************************************************= **************
Cina Foroutan-Nejad, Ph. D.
School of Chemistry, College of Science,
University of Tehran, Tehran, Iran
http://independent.academia.edu/CinaForoutanNejad




________________________________
=A0From: Elham Abdolhamidi flight.66.ab---gmail.com <owner-chemistry|,|ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus|,|yahoo.co.uk>
Sent: Wednesday, 9 May 2012, 11:32
Subject: CCL: question on Gaussview


Sent to CCL by: "Elham=A0 Abdolhamidi" [flight.66.ab~~gmail.com]
I have been working with gaussview (g09) and I have some problems in drawin= g polymers. You know, I draw the monomer and then I use PBC to make the pol= ymer. but after combining in PBC , there appears some singlet, doublet 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 prob= lem 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-= the strange characters on the top line to the |,| sign. You can also



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

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

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<html><body><div style=3D"color:#000; background-color:= #fff; font-family:arial, helvetica, sans-serif;font-size:12pt"><= div><span>Dear Elham,</span></div><div><br>= ;<span></span></div><div><span>Please do reme= mber that what you call double, triple bond etc. has no meaning in the cont= ext of ab initio or DFT (also within the context of semi-empirical theory!)= ! If you see the input file of your software, you will find NO information = regarding the "bonds"!</span></div><div><spa= n>Forget about bonds and submit your job!</span></div><di= v><br><span></span></div><div><span>= Good luck,</span></div><div><span>Cina</span>= </div><div><span>****************************************= *************************************************</span></div>&= lt;div><span>Cina Foroutan-Nejad, Ph. D.</span></div>&= lt;div><span>School of Chemistry, College of Science,</span>= </div><div><span>University of Tehran, Tehran,
=A0Iran</span></div><div><span>http://independ= ent.academia.edu/CinaForoutanNejad</span></div><div>&= lt;span><br></span></div><div><span><br= ></span></div><div><br></div> =A0<div s= tyle=3D"font-family: arial, helvetica, sans-serif; font-size: 12pt;&qu= ot;> <div style=3D"font-family: times new roman, new york, times= , serif; font-size: 12pt;"> <div dir=3D"ltr"> <f= ont face=3D"Arial" size=3D"2"> <hr size=3D"1= "> =A0<b><span style=3D"font-weight:bold;">Fr= om:</span></b> Elham Abdolhamidi flight.66.ab---gmail.com &lt;owner-= chemistry|,|ccl.net&gt= ;<br> <b><span style=3D"font-weight: bold;">To:= </span></b> "Foroutan-Nejad, Cina " &lt;canyslopu= s|,|yahoo.co.uk&gt= ; <br> <b><span style=3D"font-weight: bold;">Se= nt:</span></b> Wednesday, 9 May 2012, 11:32<br> <b>= <span style=3D"font-weight: bold;">Subject:</span><= ;/b> CCL: question on Gaussview<br> </font> </div> <= ;br><br>Sent to CCL by: "Elham&nbsp; Abdolhamidi" [f= light.66.ab~~gmail.com]&= lt;br>I have been working with gaussview (g09) and I have some problems = in
=A0drawing polymers. You know, I draw the monomer and then I use PBC to mak= e the polymer. but after combining in PBC , there appears some singlet, dou= blet and triplet bonds (which are not correct and they should not be there!= ). <br>I have also read different manuals for gaussview but I still h= ave this problem and I cannot get a good structure for the polymers.<br&= gt;I'll be so thankful if you help me solving this problem.<br>El= ham<br><br><br><br>-=3D This is automatically added= to each message by the mailing script =3D-<br>To recover the email a= ddress of the author of the message, please change<br><br>look = up the X-Original-From: line in the mail header.<br><br>E-mail = to subscribers: <a ymailto=3D"mailto:C= HEMISTRY|,|ccl.net&quo= t; href=3D"mailto:CHEMISTRY|,|ccl.net">CHEMISTRY|,|ccl.net</a> or use:<b= r>&nbsp; &nbsp; &nbsp; <a href=3D"http://www.ccl.= net/cgi-bin/ccl/send_ccl_message"
=A0target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_cc= l_message</a><br><br>E-mail to administrators: <a = ymailto=3D"mailto:CHEMISTRY-REQUE= ST|,|ccl.net" hre= f=3D"mailto:CHEMISTRY-REQUEST= |,|ccl.net">CHEMIS= TRY-REQUEST|,|ccl.net</= a> or use<br>&nbsp; &nbsp; &nbsp; <a href=3D"<= a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank= ">http://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D"= _blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</= a><br><br<br>&nbsp; &nbsp; &nbsp; <a href= =3D"http://www.ccl.net/chemistry/sub_unsub.shtml" target=3D&q= uot;_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a&= gt;<br><br>Before posting, check wait time at: <a href=3D&qu= ot;http://www.ccl.net&= quot; target=3D"_blank">http://www.ccl.net</a><br><br>Job: <a = href=3D"http://w= ww.ccl.net/jobs" target=3D"_blank">http://www.ccl.net/jobs</a> &= lt;br>Conferences: <a href=3D"http://server.ccl.ne= t/chemistry/announcements/conferences/" target=3D"_blank"= ;>http://server.ccl.net/chemistry/announcements/conference= s/</a><br><br>Search Messages: <a
=A0href=3D"http://www.ccl.net/chemistry/searchccl/index.shtml" target=3D"_blank">http://www.ccl.net/chemistry/s= earchccl/index.shtml</a><br><br>If your mail bounces = > from CCL with 5.7.1 error, check:<br>&nbsp; &nbsp; &nbsp;= <a href=3D"http://www.ccl.net/spammers.txt" target=3D"_blank"= ;>http://w= ww.ccl.net/spammers.txt</a><br><br>RTFI: <a href= =3D"http://www.ccl.net/chemistry/aboutccl/instructions/&quo= t; target=3D"_blank">http://www.ccl.net/chemistry/about= ccl/instructions/</a><br><br><br><br><= br> </div> </div> =A0</div></body></html><= /blockquote>



--
***********************= **************************
Dr. I. SARAVANAN, M.Sc., M.Phil., PGDCA., PGD= HRM., Ph.D.,
Consultant, PerkinElmer Informatics,
UVJ Technologies Pvt.Ltd, 3rd Floor ,Plot No. 16 A, Cochin Special Eco= nomic Zone (CSEZ) Seaport Airport Road, Kakkanad,
Cochin - 682 03= 7
Kerala =09
*************************************************
Re= s: No. 10, Neithal street, Solainagar, Muthialpet,
Puducherry - 605 003<= br>Cell: 9895079171
*************************************************

--e89a8f2350979dac3d04bfa73ff8-- From owner-chemistry@ccl.net Thu May 10 07:57:00 2012 From: "George Fitzgerald George.Fitzgerald{}accelrys.com" To: CCL Subject: CCL: IR Spectra (Frequency Calculation) Message-Id: <-46879-120510041218-16058-jA64+WXLB4eY9uordtNmwg- -server.ccl.net> X-Original-From: George Fitzgerald Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 10 May 2012 01:12:05 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [George.Fitzgerald=accelrys.com] Joe, You can perform a constrained optimization at each conformation of interest. When you generate the IR frequencies you might find some are imaginary if the conformation is not a local minimum. But for those that are local minima there's no problem with this procedure. If the minimum is well-defined (i.e., deep enough) you don't even need to do the constraint. I did a quick AM1 calculation on n-butane in 2 confirmations /\/ and \_/ and both geometries converged quite easily and gave slightly different frequencies. You could try forcing the conformation using a continuum or explicit solvent model, but there's no guarantee than you'll get a different conformation. And if you've used explicit solvent molecules then you've got to account for these in the IR calculation, which makes it even more expensive. -george -----Original Message----- > From: owner-chemistry+gfitzgerald==accelrys.com-,-ccl.net [mailto:owner-chemistry+gfitzgerald==accelrys.com-,-ccl.net] On Behalf Of Joe Golab joseph.golab .. ineos.com Sent: Wednesday, May 09, 2012 8:52 AM To: George Fitzgerald Subject: CCL: IR Spectra (Frequency Calculation) 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.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu May 10 18:28:00 2012 From: "Tim Cheeseright tim=cresset-group.com" To: CCL Subject: CCL: Cresset offering free training at user meeting: Cambridge, MA, May 18. Message-Id: <-46880-120510152904-9366-NObekvkw8PtvcC2CnVWvvw^-^server.ccl.net> X-Original-From: "Tim Cheeseright" Date: Thu, 10 May 2012 15:29:01 -0400 Sent to CCL by: "Tim Cheeseright" [tim|-|cresset-group.com] Hi all, Last chance to sign up for Cresset's North American User Meeting to held Friday May 18 in Cambridge, MA. Attendance is completely free. We'll be launching, demonstrating and providing training on 'Forge' - our new, powerful computational suite to understand SAR and design as well as showcasing some of the new science we've doing with our existing applications. This is an excellent opportunity to meet and network with other computational and medicinal chemists from biotech and pharma companies whilst seeing or using Cresset's software for yourself. In the morning we will provide free training, in the afternoon we have a range of excellent talks. Choose to attend either or both sessions. Numbers are limited so please register now. See http://bit.ly/LYRmMQ or contact me at address below for more information. Tim Cheeseright Director, Products Cresset BMD Ltd tim#cresset-group.com http://www.cresset-group.com