From owner-chemistry@ccl.net Fri Dec 4 12:58:00 2009 From: "Peter Khlyabich khlyabic|a|usc.edu" To: CCL Subject: CCL:G: Global minima Message-Id: <-40863-091204125651-16872-w9w9wAyG2ckNsbf69kEQBQ . server.ccl.net> X-Original-From: "Peter Khlyabich" Date: Fri, 4 Dec 2009 12:56:47 -0500 Sent to CCL by: "Peter Khlyabich" [khlyabic() usc.edu] Hey, I have two questions: 1) I'm trying to run calculations using Gaussian. In order to check if the obtained structures are the global minima I run frequency calculations. Very often the optimized structures are not in the minima but in saddle point. Is there any way to run calculations the way that they won't stop until global minima is found? 2) Also I study charge molecules. This means I study anions and cations. When I run calculation very often I get the error that convergence criteria not met and SCF is confused. To avoid this I use SCF=qc or SCF=xqc,MaxCyc=1000 but non of this methods helps. The only way i found to overcome this problem is use IOp(5/6=4). But I don't consider this as the best method. Does any one have any ideas how to overcome this message error? Appreciate your help in advance Peter From owner-chemistry@ccl.net Fri Dec 4 15:53:00 2009 From: "Ol Ga eurisco1]~[pochta.ru" To: CCL Subject: CCL:G: Global minima Message-Id: <-40864-091204142153-19073-g1HPLHiiW5mZlgPUlPutBw^^^server.ccl.net> X-Original-From: "Ol Ga" Date: Fri, 4 Dec 2009 14:21:49 -0500 Sent to CCL by: "Ol Ga" [eurisco1**pochta.ru] Dear Peter Khlyabich, 1) First, optimization procedure implemented in Gaussian searches minima which can be or can not to be global. You should compare energies of structures. To try to prevent convergence to TS (other type of stationary points) you should use route section similar to NoSymm Opt(tight,calcfc,GDIIS) Anyway, it is probable that you will find TS point in this case. And you can _guess_ that structure is global minima because full scan of PES is impossible now. 2) Are your charged structures ion-radicals? If "Yes", use keyword vshift=150 in SCF group. SCF(XQC,vshift=150) Sincerely, Ol Ga **************************** Sent to CCL by: "Peter Khlyabich" [khlyabic() usc.edu] Hey, I have two questions: 1) I'm trying to run calculations using Gaussian. In order to check if the obtained structures are the global minima I run frequency calculations. Very often the optimized structures are not in the minima but in saddle point. Is there any way to run calculations the way that they won't stop until global minima is found? 2) Also I study charge molecules. This means I study anions and cations. When I run calculation very often I get the error that convergence criteria not met and SCF is confused. To avoid this I use SCF=qc or SCF=xqc,MaxCyc=1000 but non of this methods helps. The only way i found to overcome this problem is use IOp(5/6=4). But I don't consider this as the best method. Does any one have any ideas how to overcome this message error? Appreciate your help in advance Peter From owner-chemistry@ccl.net Fri Dec 4 19:40:01 2009 From: "Andrew Orry andy a molsoft.com" To: CCL Subject: CCL: Introducing ICM-Chemist-Pro Message-Id: <-40865-091204182011-15030-Lxe+Zo4vUtScjk8dhjAMZg:server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 Dec 2009 15:14:10 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy%x%molsoft.com] You are invited to join our free webinar next week on Tuesday 8th December 9AM PST where we will introduce our latest product called ICM-Chemist-Pro. Please see this webpage http://www.molsoft.com/icm-chemist-pro.html for all the ICM-Chemist-Pro features. ICM-Chemist-Pro has a wide range of 2D and 3D chemistry features including a 3D interactive ligand editor, ligand docking, chemical superposition, chemical search, database enumeration and QSAR tools. The free registration includes a 2 week full-feature trial version of the software so you can try out what you see in the webinar. Register for the webinar here: http://www.molsoft.com/icm-chemist-pro-webinar.html Thanks, Andrew Orry Senior Scientist, MolSoft LLC (858) 625 2000 x108 From owner-chemistry@ccl.net Fri Dec 4 21:28:01 2009 From: "Daniel Glossman-Mitnik dglossman+*+gmail.com" To: CCL Subject: CCL:G: how to build a polythiophene unit cell for a pbc gaussian calculation Message-Id: <-40866-091204204136-17938-kL9rNYBxAPqsiWoHq2Pxww*server.ccl.net> X-Original-From: Daniel Glossman-Mitnik Content-Type: multipart/alternative; boundary=000325559fce64349a0479f0966a Date: Fri, 4 Dec 2009 17:48:49 -0700 MIME-Version: 1.0 Sent to CCL by: Daniel Glossman-Mitnik [dglossman:+:gmail.com] --000325559fce64349a0479f0966a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear netters: I will be pleased if you can point me to a (step by step) guide on how to build a polythiophene unit cell for a pbc gaussian calculation, using GaussView or any other program. Please note: I don=C2=B4t need only the input file, I want to learn how to = build the unit cell. Thanks in advance, Daniel ***************************************************************************= ************************************ Dr. Daniel Glossman-Mitnik: Centro de Investigaci=C3=B3n en Materiales Avanzados, SC Grupo NANOCOSMOS - Modelado Molecular y Simulaci=C3=B3n Computacional de Nanomateriales Miguel de Cervantes 120 - Complejo Industrial Chihuahua - Chihuahua, Chih 31109, Mexico Phone: +52 614 4391151 Secretary/FAX: +52 614 4394852 Lab: +52 614 4394805 E-mail: daniel.glossman*cimav.edu.mx dglossman*gmail.com WWW: http://www.cimav.edu.mx/cv/daniel.glossman http://blogs.cimav.edu.mx/daniel.glossman ***************************************************************************= ************************************ --000325559fce64349a0479f0966a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear netters:

I will be pleased if you can point me to a (step b= y step) guide on how to build a polythiophene
unit cell for a pbc gauss= ian calculation, using GaussView or any other program.
Please note: I do= n=C2=B4t need only the input file, I want to learn how to build the unit ce= ll.

Thanks in advance,

Daniel

*****************= ***************************************************************************= *******************
Dr. Daniel Glossman-Mitnik:
Centro de Investigaci= =C3=B3n en Materiales Avanzados, SC
Grupo NANOCOSMOS =C2=A0- =C2=A0Modelado Molecular y Simulaci=C3=B3n Computa= cional de Nanomateriales
Miguel de Cervantes 120 - Complejo Industrial C= hihuahua - Chihuahua, Chih 31109, Mexico
Phone: +52 614 4391151 =C2=A0 = =C2=A0 Secretary/FAX: +52 614 4394852 =C2=A0 =C2=A0 Lab: +52 614 4394805 E-mail: =C2=A0daniel.glossm= an*cimav.edu.mx =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0dglossman*gmail.com
WWW: =C2=A0http://www.cimav.edu.mx/cv/daniel.gloss= man
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0http://blogs.cimav.edu.mx/daniel.glossman*************************************************************************= **************************************
--000325559fce64349a0479f0966a-- From owner-chemistry@ccl.net Fri Dec 4 23:03:01 2009 From: "Roy Green powergreen]_[gmail.com" To: CCL Subject: CCL: Gen in gaussian Message-Id: <-40867-091204225931-24231-oqEwjiEV4zsx98DZWEnpBg++server.ccl.net> X-Original-From: Roy Green Content-Type: multipart/alternative; boundary=00c09f8994ca2503310479f2db15 Date: Fri, 4 Dec 2009 22:31:12 -0500 MIME-Version: 1.0 Sent to CCL by: Roy Green [powergreen%x%gmail.com] --00c09f8994ca2503310479f2db15 Content-Type: text/plain; charset=ISO-8859-1 Hi, All I tried to create a polar H-H' bond by altering the electronegativity of the hydrogen,H'. Of course such bond does not exist. I did this by using different orbital exponent for the basis set centered on the two atoms. I am a little confused why the H atom with large orbital exponent bears more negative charges. My understanding is that the atoms with larger orbital exponent supposed to have more negative charges,since the more compact basis set is used for that atom. Could you please give me any suggestion? The following is my input file and part of the output with the Mulliken charges. Thank you. Regards Roy cha INPUT: %chk=H.chk %nprocshared=1 %Mem=50Mb #P HF/Gen GFInput NoSymm pop=full corner 0 1 H 0.0 0.0 0.0 H 0.0 0.0 0.75 1 0 S 1 1.00 0.1000000000D+01 0.1000000000D+01 **** 2 0 S 1 1.00 0.8000000000D+00 0.1000000000D+01 **** OUTPUT: ... Atomic charges with hydrogens summed into heavy atoms: 1 1 H 0.179398 2 H -0.179398 ... --00c09f8994ca2503310479f2db15 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, All
I tried to create a polar H-H' bond by altering the electron= egativity of the hydrogen,H'. Of course such bond does not exist.
= =A0I did this by using different orbital exponent for the basis set centere= d on the two atoms. I am a little confused why the H atom with large orbita= l exponent bears more negative charges. My understanding is that the atoms = with larger orbital exponent supposed to have more negative charges,since t= he more compact basis set is used for that atom. Could you please give me a= ny suggestion?
The following is my input file and part of the output with the Mulliken cha= rges.
Thank you.

Regards

Roy
cha
=A0=A0

INPU= T:

%chk=3DH.chk
%nprocshared=3D1
%Mem=3D50Mb
#P HF/Gen GFIn= put NoSymm pop=3Dfull
=A0
corner
=A0
0 1
H 0.0 0.0 0.0
H 0.0 0.0 0.75

1 0=A0S=A0=A0 1 1.00
=A0=A0=A0=A0=A0 0.1000000000D+01=A0 0.1000000000D+01=
****
2 0
S=A0=A0 1 1.00
=A0=A0=A0=A0=A0 0.8000000000D+00=A0 0.= 1000000000D+01
****

OUTPUT:
...
=A0Atomic charges with hydrogens summed into heavy atoms:
=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 1
=A0=A0=A0=A0 1=A0 H=A0=A0=A0 0.17939= 8
=A0=A0=A0=A0 2=A0 H=A0=A0 -0.179398
...

--00c09f8994ca2503310479f2db15--