From owner-chemistry@ccl.net Thu Sep 27 03:15:00 2007 From: "Alain Borel alain.borel,+,epfl.ch" To: CCL Subject: CCL: EPR/ESR simulations Message-Id: <-35260-070927031336-1255-fgmcqWsJBX3C35vqwQRwUA###server.ccl.net> X-Original-From: Alain Borel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 Sep 2007 08:13:21 +0200 MIME-Version: 1.0 Sent to CCL by: Alain Borel [alain.borel:-:epfl.ch] Steve Bowlus chezbowlus : comcast.net wrote: > > Sent to CCL by: Steve Bowlus [chezbowlus]^[comcast.net] > This is new for me - > Can someone point me to a program that will calculate and display a > simulated EPR Spectrum? We can already calculate the g-tensor, > A-tensor, and Q-tensor. What else might be needed? We are particularly > interested in EPR of iron-containing compounds. Are you considering solid-state (crystal, powder, glass) spectra, or solution spectra as well? In the former case, there are a number of programs and/or codes that you can use: http://tools.niehs.nih.gov/stdb/esdb.cfm?pagetype=LIST If you want some dynamics as well, your choice will be more limited, but the Easyspin toolkit could be a good choice, assuming that you have access to a Matlab license: http://www.easyspin.ethz.ch/ Best regards, Alain Borel Bibliothèque Scientifique Commune UNIL-EPFL BCH 2201 EPFL - SB - SCGC-BCH 1015 Lausanne, Switzerland. Tel.: +41 21 693 9800 Fax.: +41 21 693 9805 e-mail: alain.borel*epfl.ch http://biscom.epfl.ch From owner-chemistry@ccl.net Thu Sep 27 04:43:01 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas+*+chem.elte.hu" To: CCL Subject: CCL:G: Relaxed PES in g03 using forcefield? Message-Id: <-35261-070927043027-29343-9ZBvrVZTzxE/BeRoZ6Ga8Q:-:server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Type: multipart/alternative; boundary="=-rUraUAvZcFHMghmnm9An" Date: Thu, 27 Sep 2007 10:28:39 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas%%chem.elte.hu] --=-rUraUAvZcFHMghmnm9An Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Hi Ben, I list a few facts about the ModRedundant option and optimization algorithms in Gaussian, which might help you sorting out your problem: 1. I advise using redundant internal coordinates for PES scans. 2. There are default optimizers for different levels: - MM optimizer is used for MM and ONIOM microiterations for the lowest level MM calculation. ModRedundant option DOES NOT work but atoms in Cartesians can be frozen via placing -1 after the atom symbol in the geometry part of the input. At least 3 atoms should be frozen in Cartesians to avoid side effects. There is no option to turn this algorithm on for other methods, Opt=NoMicro turns off ONIOM microiterations and Opt=Large or.Opt=Small will lead to using redundant internal coordinates even for MM calculations to allow the ModRedundant option. Since using redundant internals for very large systems may be costly for MM, an MM/MM ONIOM with microiterations and selecting the atoms which are involved in ModRedundant for the "high" level allows doing PES scans for pure MM calculations. In this case if both levels use the same MM setup the result will be identical to using a simple MM calculation for the whole system. - Large molecular optimizer is default for semiempiricals, advised for large molecules or ONIOM calculations in conjunction with NoMicro. Opt=Large turns this option on for any calculation, Opt=(NoMicro, Large) is necessary to use it for whole system optimization with ONIOM QM/MM jobs. Opt=ModRedundant works with this method. - Regular optimizer is usually the default and advised for QM calculations and as the main optimizer for ONIOM jobs. Since only the higher level atoms are treated with this optimizer in an ONIOM QM/MM job by default is is advised to include all atoms belonging to ModRedundant lines into the high level explicitly. 3. The QM/MM ONIOM calculations use MM microiterations and both, freezing atoms in the Cartesian space and using ModRedundant for the high level can be used. Best wishes, Ödön - On Tue, 2007-09-25 at 10:23 -0700, Ben King king:-:chem.unr.edu wrote: > Sent to CCL by: Ben King [king^chem.unr.edu] > Dear CCLers: > > Summary: how can one use gaussian to perform a relaxed potential > energy scan with a force field? > > We need to generate a 2-D potential energy surface for a bond- > breaking coupled with a torsion. Gaussian's tools for performing a > relaxed PES using the modredundant option to opt are ideal, but Z- > matrix tools could also work. Here is the problem: Gaussian (g03) > completely ignores any constraints when we use molecular mechanics > (amber, uff, etc.), using either Z-matrices or opt=modredundant. > This also happens in OMION methods using a MM fragment. Our syntax > is correct, as we do these same calculations (albeit inaccurately and > only over limited portions of the PES) using semi-empirical methods. > > We must use a molecular mechanics force field: van der Waals > interaction are important in our molecule and we need to study the > portion of the bond dissociation region that is poorly described by > single references wavefunctions (e.g., C-C bond distances of 1.4 A to > 6.0 A in 0.2 A increments). The molecule is large (C62H38), so high- > level ab initio methods are prohibitively time consuming. Molecular > mechanics will give us the most realistic description of the > molecular behavior, provided that we use a Morse potential for the > bond dissociation. > > If anyone can suggest a procedure to generate a PES from a force > field, I would be grateful. This is one of those irritating things > that should be easy but ends up being exceptionally difficult. > Also, if anyone knows why Gaussian behaves so oddly with MM methods, > I would be delighted to know. > > Thanks, > > Ben > > p.s. The version of Gaussian is: Gaussian 03: AM64L-G03RevC.02 12- > Jun-2004 > p.p.s. We are limping through this by running thousands of > individual constrained optimizations using Tinker, but it isn't > pretty... > > ---- > Benjamin T. King, Associate Professor > Department of Chemistry/216 > University of Nevada, Reno 89557 > tel (775) 784-1736 fax (775) 784-6804 > king^_^chem.unr.edu > http://www.chem.unr.edu/faculty/btk/> > > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas --=-rUraUAvZcFHMghmnm9An Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit Hi Ben,

I list a few facts about the ModRedundant option and optimization algorithms in Gaussian, which might help you sorting out your problem:
1. I advise using redundant internal coordinates for PES scans.
2. There are default optimizers for different levels:
- MM optimizer is used for MM and ONIOM microiterations for the lowest level MM calculation. ModRedundant option DOES NOT work but atoms in Cartesians can be frozen via placing -1 after the atom symbol in the geometry part of the input. At least 3 atoms should be frozen in Cartesians to avoid side effects. There is no option to turn this algorithm on for other methods, Opt=NoMicro turns off ONIOM microiterations and Opt=Large or.Opt=Small will lead to using redundant internal coordinates even for MM calculations to allow the ModRedundant option. Since using redundant internals for very large systems may be costly for MM, an MM/MM ONIOM with microiterations and selecting the atoms which are involved in ModRedundant for the "high" level allows doing PES scans for pure MM calculations. In this case if both levels use the same MM setup the result will be identical to using a simple MM calculation for the whole system.
- Large molecular optimizer is default for semiempiricals, advised for large molecules or ONIOM calculations in conjunction with NoMicro. Opt=Large turns this option on for any calculation, Opt=(NoMicro, Large) is necessary to use it for whole system optimization with ONIOM QM/MM jobs. Opt=ModRedundant works with this method.
- Regular optimizer is usually the default and advised for QM calculations and as the main optimizer for ONIOM jobs. Since only the higher level atoms are treated with this optimizer in an ONIOM QM/MM job by default is is advised to include all atoms belonging to ModRedundant lines into the high level explicitly.
3.    The QM/MM ONIOM calculations use MM microiterations and both, freezing atoms in the Cartesian space and using ModRedundant for the high level can be used.

Best wishes,

Ödön
-
On Tue, 2007-09-25 at 10:23 -0700, Ben King king:-:chem.unr.edu wrote: 
Sent to CCL by: Ben King [king^chem.unr.edu]
Dear CCLers:

Summary:  how can one use gaussian to perform a relaxed potential  
energy scan with a force field?

We need to generate a 2-D potential energy surface for a bond- 
breaking coupled with a torsion.  Gaussian's tools for performing a  
relaxed PES using the modredundant option to opt are ideal, but Z- 
matrix tools could also work.  Here is the problem:  Gaussian (g03)  
completely ignores any constraints when we use molecular mechanics  
(amber, uff, etc.), using either Z-matrices or opt=modredundant.   
This also happens in OMION methods using a MM fragment.  Our syntax  
is correct, as we do these same calculations (albeit inaccurately and  
only over limited portions of the PES) using semi-empirical methods.

We must use a molecular mechanics force field: van der Waals  
interaction are important in our molecule and we need to study the  
portion of the bond dissociation region that is poorly described by  
single references wavefunctions (e.g., C-C bond distances of 1.4 A to  
6.0 A in 0.2 A increments). The molecule is large (C62H38), so high- 
level ab initio methods are prohibitively time consuming.  Molecular  
mechanics will give us the most realistic description of the  
molecular behavior, provided that we use a Morse potential for the  
bond dissociation.

If anyone can suggest a procedure to generate a PES from a force  
field, I would be grateful. This is one of those irritating things  
that should be easy but ends up being exceptionally difficult.   
Also,  if anyone knows why Gaussian behaves so oddly with MM methods,  
I would be delighted to know.

Thanks,

Ben

p.s.  The version of Gaussian is: Gaussian 03:  AM64L-G03RevC.02 12- 
Jun-2004
p.p.s.  We are limping through this by running thousands of  
individual constrained optimizations using Tinker, but it isn't  
pretty...

----
Benjamin T. King, Associate Professor
Department of Chemistry/216
University of Nevada, Reno 89557
tel (775) 784-1736 fax (775) 784-6804
king^_^chem.unr.edu
http://www.chem.unr.edu/faculty/btk/








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-- 
Ödön Farkas
Associate professor
Deparment of Organic Chemistry and
Laboratory of Chemical Informatics,
Institute of Chemistry,
Eötvös Loránd University, Budapest
Address: 1/A Pázmány Péter sétány,
H-1117 Budapest, Hungary
Phone: +36-1-372-2570
Cell phone: +36-30-255-3111
Fax: +36-1-372-2620
URL: http://organ.elte.hu/farkas
--=-rUraUAvZcFHMghmnm9An-- From owner-chemistry@ccl.net Thu Sep 27 05:42:01 2007 From: "Frank Neese neese~!~thch.uni-bonn.de" To: CCL Subject: CCL: EPR/ESR simulations Message-Id: <-35262-070927045823-3904-ZxR7bgJTw4pHDlm1kqfiUg##server.ccl.net> X-Original-From: Frank Neese Content-Type: multipart/alternative; boundary=Apple-Mail-21--24601855 Date: Thu, 27 Sep 2007 10:57:59 +0200 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Frank Neese [neese . thch.uni-bonn.de] --Apple-Mail-21--24601855 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Dear Alain, ages ago i had written a windows program to do this and it was used a =20= lot by the EPR community. I am not sure whether it still runs on =20 modern computers but you are welcome to try. Apparently the most =20 modern (non-comercial) program is "EasySpin" by Stefan Portmann =20 (previously in Z=FCrich; http://www.easyspin.ethz.ch/). the most modern =20= commercial program is from Graeme Hanson (XSophe) and is sold via =20 Bruker. For High-spin iron compounds you probably also want to calculate the =20 zero-field splitting parameters and the orca program is particularly =20 adapted to this purpose (http://www.thch.uni-bonn.de/tc/orca/). Best regards, Frank > Sent to CCL by: Alain Borel [alain.borel:-:epfl.ch] > Steve Bowlus chezbowlus : comcast.net wrote: >> Sent to CCL by: Steve Bowlus [chezbowlus]^[comcast.net] >> This is new for me - >> Can someone point me to a program that will calculate and display =20 >> a simulated EPR Spectrum? We can already calculate the g-tensor, =20 >> A-tensor, and Q-tensor. What else might be needed? We are =20 >> particularly interested in EPR of iron-containing compounds. --------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl fuer Theoretische Chemie Universitaet Bonn Wegelerstr. 12 D-53115 Bonn, Germany neese#,#thch.uni-bonn.de Phone: +49-28-732351 FAX: +49-(0)228-739064 --------------------------------------------------------------- --Apple-Mail-21--24601855 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Dear Alain,

ages ago i had written a = windows program to do this and it was used a lot by the EPR community. I = am not sure whether it still runs on modern computers but you are = welcome to try. Apparently the most modern (non-comercial) program is = "EasySpin" by Stefan Portmann (previously in Z=FCrich; http://www.easyspin.ethz.ch/). = the most modern commercial program is from Graeme Hanson (XSophe) and is = sold via Bruker.=A0
For High-spin iron compounds you probably = also want to calculate the zero-field splitting parameters and the orca = program is particularly adapted to this purpose (http://www.thch.uni-bonn.de/= tc/orca/).
Best = regards,
Frank
=A0

Sent to CCL by: Alain Borel = [alain.borel:-:epfl.ch]
Steve Bowlus = chezbowlus : comcast.net wrote:
Sent to CCL by: Steve Bowlus = [chezbowlus]^[comcast.net]
This is new = for me -
Can someone point me to a = program that will calculate and display a simulated EPR Spectrum?=A0 We can already calculate the = g-tensor, A-tensor, and Q-tensor. What else might be needed?=A0 We are particularly = interested in EPR of iron-containing = compounds.

neese#,#thch.uni-bonn.de
Phone: = +49-28-732351
FAX:=A0+49-(0)228-739064
---------------= ------------------------------------------------


=
= --Apple-Mail-21--24601855-- From owner-chemistry@ccl.net Thu Sep 27 11:30:00 2007 From: "Barry Hardy barry.hardy---vtxmail.ch" To: CCL Subject: CCL: Predictive ADME/Toxicology meeting and workshop (17-19 October 2007) Message-Id: <-35263-070927111146-5195-HMXrxJ2fZMORFvJNPL+Uyw:-:server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="------------050904000506070401090202" Date: Thu, 27 Sep 2007 16:10:55 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy=vtxmail.ch] This is a multi-part message in MIME format. --------------050904000506070401090202 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit We are holding conference and workshop sessions on Predictive ADME/Toxicology, including discussions of new collaborative research projects and potential for cooperations, at the upcoming joint eCheminfo-InnovationWell Autumn 2007 community of practice meeting to be held at Bryn Mawr College, Philadelphia. The sessions will run 17-19 October. Poster Session We will be running poster sessions in the evenings at the meeting. Please send your abstract ca. 300-500 words to eCheminfo -(at)- douglasconnect.com for approval. More information on the program is available at http://echeminfo.com/COMTY_admeforumbm07 Contact for registration: Nicki.Douglas -(at)- douglasconnect.com A 50% academic discount is available. best regards Barry Hardy Barry Hardy, PhD Douglas Connect Switzerland Tel: +41 61 851 0170 Blog: http://barryhardy.blogs.com/cheminfostream/ --------------050904000506070401090202 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
We are holding conference and workshop sessions on Predictive ADME/Toxicology, including discussions of new collaborative research projects and potential for cooperations, at the upcoming joint eCheminfo-InnovationWell Autumn 2007 community of practice meeting to be held at Bryn Mawr College, Philadelphia.  The sessions will run 17-19 October. 

Poster Session
We will be running poster sessions in the evenings at the meeting. Please send your abstract ca. 300-500 words to eCheminfo -(at)- douglasconnect.com for approval.

More information on the program is available at http://echeminfo.com/COMTY_admeforumbm07

Contact for registration: Nicki.Douglas -(at)- douglasconnect.com  A 50% academic discount is available. 

best regards
Barry Hardy

Barry Hardy, PhD
Douglas Connect
Switzerland
Tel: +41 61 851 0170
Blog: http://barryhardy.blogs.com/cheminfostream/
--------------050904000506070401090202-- From owner-chemistry@ccl.net Thu Sep 27 21:52:01 2007 From: "Kadir Diri kadir|a|visual1.chem.pitt.edu" To: CCL Subject: CCL: Electronic structure and quantum chemistry forum Message-Id: <-35264-070927214900-10759-zLrP9BhtLs7d5nt59tzycA#server.ccl.net> X-Original-From: Kadir Diri Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 Sep 2007 18:03:32 -0700 MIME-version: 1.0 Sent to CCL by: Kadir Diri [kadir[A]visual1.chem.pitt.edu] Dear Colleagues, We are delighted to announce the opening of an Electronic Structure and Quantum Chemistry forum to promote the dissemination of new results and ideas, technical information and know-how, discussions, and forging collaborations. We are excited to contribute in spreading the fun of learning theory and playing with electronic structure. The forum can be accessed through the Center for Computational Studies of Electronic Structure and Spectroscopy of Open-Shell and Electronically Excited Species (iOpenShell) web site: http://iopenshell.usc.edu/forum Our vision is that the forum will serve a broad scientific community ranging from quantum chemistry rookies to seasoned gurus. The forum welcomes experimentalists who wish to enhance their research by using ab initio tools and are looking for advice or help on technical issues, experienced computational chemists who would like to learn about new developments, developers of electronic structure codes and methods who want to share their most recent results, as well as conference organizers, prospective employers with job ads, and so on. We are looking forward to your valuable contributions to this undertaking. Best regards, The iOpenShell Team