From owner-chemistry@ccl.net Thu Dec 17 06:43:01 2009 From: "Ashwini Bundhun ashwinibilly#,#hotmail.com" To: CCL Subject: CCL: Optimization problems Message-Id: <-40932-091217024938-3132-BD4hHRCAZ8uGtGeniPptCA(!)server.ccl.net> X-Original-From: "Ashwini Bundhun" Date: Thu, 17 Dec 2009 02:49:34 -0500 Sent to CCL by: "Ashwini Bundhun" [ashwinibilly(a)hotmail.com] Dear ALL I am trying to optimize the F-Ge-CI3 molecule, where the divalent Ge atom is bonded to the F and C atoms, and the C atom is bonded to the three iodine atoms. The computation ends normally. It is observed that one of the iodine atom leaves the C atom and gets bonded to the Ge atom. Also the bond between Ge and C is broken. However, when the carbon atom is bonded to halogens like F and Cl this problem is not encountered at all. For the iodine atom, the 6-311G(d,p) and LANL2DZ ECP basis sets are used. Has anyone encountered this problem? Any advise? Thanks Ashwini From owner-chemistry@ccl.net Thu Dec 17 08:05:00 2009 From: "case case===biomaps.rutgers.edu" To: CCL Subject: CCL: zinc parameter for gaff in QM/MM(gaussian) Message-Id: <-40933-091216225605-25185-IT5yU+aQlyxYptlx98PlNA]|[server.ccl.net> X-Original-From: case Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 16 Dec 2009 22:23:42 -0500 Mime-Version: 1.0 Sent to CCL by: case [case%biomaps.rutgers.edu] On Wed, Dec 16, 2009, Bill Ross ross(~)cgl.ucsf.edu wrote: > > Sent to CCL by: Bill Ross [ross^^cgl.ucsf.edu] > > Here is the Zinc ion parameters; sigma= 1.70 and epsion=0.67 > > I believe that sigma is different from R* used by amber. Here > is some discussion of ion param types, but it doesn't mention > the sigma convention: > > http://ambermd.org/Questions/vdw.html > > By the way, has anyone seen "Parameters of Monovalent Ions > in the AMBER-99 Forcefield: Assessment of Inaccuracies and > Proposed Improvements" http://pubs.acs.org/doi/abs/10.1021/jp0765392 > They claim, "These errors arise from an ad hoc adaptation of �qvist's > cation parameters." It seems their understanding of the > combining rules used by different force fields is flawed, > in that this was used in adapting Aqvist to Amber. On the other > hand, they claim to fix observed problems in simulations, so that > is interesting. > > Here is some discussion of the conversion of Aqvist params for Amber: > http://pubs.acs.org/doi/abs/10.1021/j100084a050 While the above papers are certainly of interest, CCL readers should also be aware of the paper that describes the current Amber monovalent ion potentials (there are separate sets of parameters for use with SPC/E, TIP3P and TIP4Pew water models): %A I.S. Joung %A T.E. Cheatham, III %T Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations %J J. Phys. Chem. B %V 112 %P 9020-9041 %D 2008 The issues mentioned above are discussed at length in this paper. ...dave case From owner-chemistry@ccl.net Thu Dec 17 08:39:01 2009 From: "dolkeen Zaft dolkeen::hotmail.com" To: CCL Subject: CCL:G: G03 input file Message-Id: <-40934-091215133332-26846-c6EHEPHW19INTVPoDCdd4g-#-server.ccl.net> X-Original-From: dolkeen Zaft Content-Type: multipart/alternative; boundary="_fb54b478-70f3-4222-93ab-e1de01bd1ef4_" Date: Tue, 15 Dec 2009 18:00:43 +0000 MIME-Version: 1.0 Sent to CCL by: dolkeen Zaft [dolkeen|-|hotmail.com] --_fb54b478-70f3-4222-93ab-e1de01bd1ef4_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Mr.M.IBRAHIM =20 Thanks=20 I tried it and workd =20 =20 I need your kind assistance to show me how to get the enthalpy of Formation= at 298 for a new compound : (CH3)4As2 using Gaussian 03 =2C as using the p= rocedures to obtain thermal properties of Liquid Arsenic not possible using= G03 =20 I succeeded to make best draw for compound using Gauss View anbd got all ne= cessary thermal properties such as Energy=2CEntropy as wellas Cv =2Cfor Met= hane it is available=20 =20 Is it possible toget complete calculation toget enthalpy for each compounds= =20 =20 4CH4+2As(liquid) =3D(Ch3)2As-As-(CH3)2 + 2H2=20 =20 Need the gibbs ewnergy tojudge if reaction will be spontanious "as intermed= iate product " =20 Appreciating kind assistance=20 =20 O.Akoubeh =20 > From: owner-chemistry[a]ccl.net To: dolkeen[a]hotmail.com Subject: CCL: G03 input file Date: Mon=2C 14 Dec 2009 11:53:27 +0000 Dear Ossama You can use the following obvious keywords: Temperature=3DXXX=E1 Pressure=3DYYY=20 where XXX is the desired temperature in Kelvin1 and YYY is the desired pres= sure in atmosphere. Sincerely=3B=20 M. Ibrahim On Sat=2C Dec 12=2C 2009 at 10:33 AM=2C osama Tawfeeq Akoubeh dolkeen=2Chot= mail.com wrote: Sent to CCL by: "osama Tawfeeq Akoubeh" [dolkeen^hotmail.com] Hi anyone know how to change the condition of generating thermodynamic propert= ies at other than STP : selected temperature and pressure thanks -=3D This is automatically added to each message by the mailing script =3D-=
Dear Mr.M.IBRAHIM
 =3B
Thanks
I tried it and workd
 =3B
 =3B
I need your kind assistance to show me how to get the enthalpy of Formation= at 298 for a new compound : (CH3)4As2 using Gaussian 03 =2C as using the p= rocedures to obtain thermal properties of Liquid Arsenic not possible using= G03
 =3B
I succeeded to make best draw for compound using Gauss = View anbd got all necessary thermal properties such as Energy=2CEntropy as = wellas Cv =2Cfor Methane it is available
 =3B
Is it possible tog= et complete calculation toget enthalpy for each compounds
 =3B
4= CH4+2As(liquid) =3D(Ch3)2As-As-(CH3)2 + 2H2
 =3B
Need the gibbs = ewnergy tojudge if reaction will be spontanious "as intermediate product "<= BR> =3B
Appreciating =3B kind assistance
 =3B
O.Akoub= eh


 =3B
> From: owner-chemistry[a]ccl.net
To: dolkeen[a]hotmail.com
Subject: CCL: G= 03 input file
Date: Mon=2C 14 Dec 2009 11:53:27 +0000

Dear Ossama=
You can use the following obvious keywords:
Temperature=3DXXX=E1 Pre= ssure=3DYYY
where XXX is the desired temperature in Kelvin1 and YYY is = the desired pressure in atmosphere.
Sincerely=3B
M. Ibrahim

On Sat=2C Dec 12=2C 2009 at 10:33 AM=2C osama T= awfeeq Akoubeh dolkeen=2Chotmail.com <=3Bowner-chem= istry-x-ccl.net>=3B wrote:

Sent to = CCL by: "osama Tawfeeq Akoubeh" [dolkeen^ho= tmail.com]
Hi
anyone know how to change the condition of generati= ng thermodynamic properties at other than STP : selected temperature and pr= essure


thanks



-=3D This is automatically added to= each message by the mailing script =3D-<=3Bbr


E-mail to subsc= ribers: CHEMISTRY-x-ccl.net or u= se:
=E1 =E1 =E1http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to adm= inistrators: CHEMISTRY-REQUE= ST-x-ccl.net or use
=E1 =E1 =E1http://www.ccl.net/cgi-bin/ccl/send_ccl_message<= BR>
Subscribe/Unsubscribe:
=E1 =E1 =E1http://www.ccl.net/chemistry/sub_unsub.shtml<= BR>
Before posting=2C check wait time at: http://www.ccl.net

Job: ht= tp://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/annou= ncements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchcc= l/index.shtml
<=3Bbr
=E1 =E1 =E1http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemi= stry/aboutccl/instructions/





--
=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1Mahmoud A. A. Ibrahim = =E1 =E1 =E1 =E1
=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 Current Add= ress
=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 7.05=2C School of Chemistry=2C
= =E1 =E1 =E1 =E1 =E1 =E1 =E1The University of Manchester=2C
=E1 =E1 =E1 = =E1 Oxford Road=2C Manchester=2C M13 9PL=2C
=E1 =E1 =E1 =E1 =E1 =E1 =E1= =E1 =E1 =E1 =E1 United Kingdom.

=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1= =E1 =E1 =E1Home Address
=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1Chemistry De= partment=2C
=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 Faculty of Science= =2C
=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1Minia University=2C=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 Minia 61519=2C
=E1= =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1Egypt.

= =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 Contact Information
=E1 =E1 =E1 = =E1 =E1 Email: m.ibrahim-x-comp= chem.net
=E1 =E1 =E1 =E1 =E1 =E1 =E1Website: www.compchem.net
=E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 =E1 F= ax No.: +20862342601

Windows Live: Friends get your Flickr=2C Yelp=2C and Digg updates whe= n they e-mail you. = --_fb54b478-70f3-4222-93ab-e1de01bd1ef4_-- From owner-chemistry@ccl.net Thu Dec 17 10:32:01 2009 From: "Jon Mikel Azpiroz Apezetxea jmkimteo,hotmail.com" To: CCL Subject: CCL: Transition Dipole Moments with Gaussian Message-Id: <-40935-091217061424-11710-0+AbhS9wttQ/mlzuVX9k4Q**server.ccl.net> X-Original-From: "Jon Mikel Azpiroz Apezetxea" Date: Thu, 17 Dec 2009 06:14:19 -0500 Sent to CCL by: "Jon Mikel Azpiroz Apezetxea" [jmkimteo**hotmail.com] Dear All, I am doing DFT calculations with the B3LYP hybrid functional and I would like to calculate transition dipole integrals in the molecular/atomic basis in order to estimate the probability of the electronic transition between electronic states. I supose that these type of integrals are calculated during the calculation, but I wonder how to print them. Could anyone help me? Thank you in advance. Jon Mikel Azpiroz From owner-chemistry@ccl.net Thu Dec 17 16:07:02 2009 From: "errol lewars elewars(-)trentu.ca" To: CCL Subject: CCL: Optimization problems Message-Id: <-40936-091217113126-31563-6hgIRLTauDmQzBOHDi/flQ[]server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Dec 2009 10:59:23 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars,,trentu.ca] 2009 Dec 17 Is it a problem? Maybe F-Ge-CI3 is not a stationary poin t on the PES, at least at your computational level. A hint may come from this: compare the bond energies of C-X, where X=I and X=Cl or F E. Lewars == Ashwini Bundhun ashwinibilly#,#hotmail.com wrote: > Sent to CCL by: "Ashwini Bundhun" [ashwinibilly(a)hotmail.com] > Dear ALL > > I am trying to optimize the F-Ge-CI3 molecule, where the divalent Ge atom is bonded to the F and C atoms, and the C atom is bonded to the three iodine atoms. > > The computation ends normally. > > It is observed that one of the iodine atom leaves the C atom and gets bonded to the Ge atom. Also the bond between Ge and C is broken. > > However, when the carbon atom is bonded to halogens like F and Cl this problem is not encountered at all. > > For the iodine atom, the 6-311G(d,p) and LANL2DZ ECP basis sets are used. > > Has anyone encountered this problem? > Any advise? > Thanks > > Ashwini> > > From owner-chemistry@ccl.net Thu Dec 17 21:45:01 2009 From: "david.giesen#,#kodak.com" To: CCL Subject: CCL:G: Python Gaussian Frequency Visualizer Message-Id: <-40937-091217161513-31248-e+yT/sVbQ3f5Rc8jc6k6eg[A]server.ccl.net> X-Original-From: david.giesen(a)kodak.com Content-Type: multipart/related; boundary="=_related 006D7C658525768F_=" Date: Thu, 17 Dec 2009 14:55:52 -0500 MIME-Version: 1.0 Sent to CCL by: david.giesen,+,kodak.com This is a multipart message in MIME format. --=_related 006D7C658525768F_= Content-Type: multipart/alternative; boundary="=_alternative 006D7C658525768F_=" --=_alternative 006D7C658525768F_= Content-Type: text/plain; charset="US-ASCII" To honor the memory of Warren Delano, and to thank Jan as well as the CCL and Python communities for all their free support over the years, I have submitted a program to the CCL archives that allows one to plot vibrational spectra resulting from Gaussian frequency calculations, show the molecule, and use it to animate the vibrations. The zip file contains both a Windows executable file and all the Python source code. While I hope some people find the program useful by itself, I also hope some might find the Python code useful as well. As such, the Python code I have included in the source code directory is free of any use restrictions - there are many customized Tkinter widgets as well as a class that can be used to display a rotatable molecule on any Tkinter canvas. The link to this program is: http://www.ccl.net/cca/software/Python/Gaussian_Frequency_Visualizer/ And while I thank Kodak for generously allowing me to make this code public, I also must point out that Kodak does not provide any warranty, nor does it bear responsibility for the result of any use of the code provided. Dave Giesen David J. Giesen | Research Scientist | FPEG US Display OLED Materials R+D | Eastman Kodak Company | 2/83/KRL MC02216 | Rochester, NY 14650 | david.giesen#%#kodak.com | 1-585-588-0480 Office | www.kodak.com --=_alternative 006D7C658525768F_= Content-Type: text/html; charset="US-ASCII" To honor the memory of Warren Delano, and to thank Jan as well as the CCL and Python communities for all their free support over the years, I have submitted a program to the CCL archives that allows one to plot vibrational spectra resulting from Gaussian frequency calculations, show the molecule, and use it to animate the vibrations.  The zip file contains both a Windows executable file and all the Python source code.  While I hope some people find the program useful by itself, I also hope some might find the Python code useful as well.  As such, the Python code I have included in the source code directory is free of any use restrictions - there are many customized Tkinter widgets as well as a class that can be used to display a rotatable molecule on any Tkinter canvas.

The link to this program is:

http://www.ccl.net/cca/software/Python/Gaussian_Frequency_Visualizer/

And while I thank Kodak for generously allowing me to make this code public, I also must point out that Kodak does not provide any warranty, nor does it bear responsibility for the result of any use of the code provided.
 
Dave Giesen

David J. Giesen | Research Scientist | FPEG US Display OLED Materials R+D |
Eastman Kodak Company | 2/83/KRL MC02216 | Rochester, NY 14650 |
david.giesen#%#kodak.com | 1-585-588-0480 Office |
www.kodak.com

--=_alternative 006D7C658525768F_=-- --=_related 006D7C658525768F_= Content-Type: image/gif Content-ID: <_1_08482B9808243B18006D7C658525768F> Content-Transfer-Encoding: base64 R0lGODlhWAIeAIQAAO4yJO9KQfBfWPFwa/J/e/OOivSbl/anpPeysPi9u/nIxvrS0Pvb2vzl5P27 MP3u7f729v///wAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACH5BAEA ABEALAAAAABYAh4AQAX+YCSOZGmeaKqubOu+cCzPdG3feK7vfO//OoaQ8SA1hozG7UBoKlzMphJI rVqv2Kx2y+16v16AeCweQEgIsgBhCJCLBvKATQYgRIcEkaEYjO8EYwwJZAZgh4iJiouMjY6PWGR3 IoFkDQp1ZAFFInGZZWcQfp8AhhGVAAwRDXVTkK+wsbKztLW2t7i5uru8vb6wkhFpYwFnOKiTLKiq v83Oz9DR0iySB60RDGTGIsMABNljJdZidGICBwjl3qefxdPv8PHy8/RYDvf4+fr7/P3+/wADChxI sKDBgwgTKlzIsKHDhxAjSpxIsaLFi/rqadzIsWO8YBEguPlzjGSLZR7+U6pcybIZmQMCyCQwMirT ASMjSU1CVecJOzGqRJFh1rKo0aNIs5ACUGDEA0skPDEFJ4aTiAIkG/CsQ+BnHTNJw4odS1ZGsAY5 mUbA+ofBgpoAFkSoGUDPW2JeDZx5UNPQMp6mygoeTBgpEqsRHiBhYIxBOgQKEJdwnC7yiQcKHi/Y tmrItsWcC4seTbq0F4yoU6tezbq169ewY8ueTRuh6du4c78CGWFBHbk2kLlAqbu48eOQQPLsWpLc cEHIo0ufvkUSK6gkEtA1QHQEBAQxy4S3IyIBzwAFiBJv8BjBTOrw48t/oYlMU+/jP016kFY/paVF oCQVAD7NZ+CBB5K5IgBn4923ikwRFDICVeSJoFhm6nSFCiFjMIfghyBOR8ZW71FYQjffkHHiH2gt tc5WYgAX4ow05hYMXAtGaFJI4x3w1BjvhZQTA8Rh06FXcA1Q45JMFgYSh0BS+Alzvrl4RzekqLKM SGQU2OSXYLbEG5djLLhAfmLoVcKZNm0DwYBiBJAMcVAC4E6YeOap55589unnn4AGKuighBYqWm2I Jqrooow26uijkEYq6aSUVmrppZhmqulEIQAAOw== --=_related 006D7C658525768F_=-- From owner-chemistry@ccl.net Thu Dec 17 22:21:01 2009 From: "Jimmy Stewart MrMOPAC * openmopac.net" To: CCL Subject: CCL: Improved intermolecular interactions in MOPAC2009 Message-Id: <-40938-091217195850-26505-Z14ZLPry3+EE7fzEMGp6rw%x%server.ccl.net> X-Original-From: Jimmy Stewart Content-Type: multipart/alternative; boundary="=====================_112867765==.ALT" Date: Thu, 17 Dec 2009 17:26:36 -0700 Mime-Version: 1.0 Sent to CCL by: Jimmy Stewart [MrMOPAC=openmopac.net] --=====================_112867765==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed The hydrogen bonding and dispersion correction method, developed by M. Korth, et. al. has been added to MOPAC2009. For the S26 set of interactions (see: http://www.begdb.com/) this reduces the average unsigned interaction energy error from 3.17 kcal/mol to 0.37 kcal/mol. For more information, see: "A Transferable H-bonding Correction For Semiempirical Quantum-Chemical Methods" Martin Korth, Michal Pitonak, Jan Rezac and Pavel Hobza J. Chem. Theory Comput. (http://pubs.acs.org/doi/abs/10.1021) ( -,- -,- ) .-----------------oOOo----(_)----oOOo--------------------------------------. | James J. P. Stewart | | | Stewart Computational Chemistry | E-mail: MrMOPAC-,-OpenMOPAC.net | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W | | Colorado Springs CO 80921-2512 | http://openmopac.net/ | | USA | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200| | .ooo0 | Phone: USA +(719) 488-9416 | | ( ) Oooo.| | .-----------------------\ (----( )---------------------------------------. \_) ) / (_/ --=====================_112867765==.ALT Content-Type: text/html; charset="us-ascii" The hydrogen bonding and dispersion correction method, developed by M. Korth, et. al.  has been added to MOPAC2009.  For the S26 set of interactions (see: http://www.begdb.com/) this reduces the average unsigned interaction energy error from 3.17 kcal/mol to 0.37 kcal/mol.
 
For more information, see: “A Transferable H-bonding Correction For Semiempirical Quantum-Chemical Methods” Martin Korth, Michal Pitonak, Jan Rezac and Pavel Hobza J. Chem. Theory Comput. ( http://pubs.acs.org/doi/abs/10.1021)



                         ( -,- -,- )
 .-----------------oOOo----(_)----oOOo--------------------------------------.
 | James J. P. Stewart               |                                      |
 | Stewart Computational Chemistry   | E-mail:  MrMOPAC-,-OpenMOPAC.net       |
 | 15210 Paddington Circle           |  39/03/15 N, 104/49/29 W             |
 | Colorado Springs CO 80921-2512    | http://openmopac.net/                 |
 | USA                               | SKYPE: Jimmy.Stewart2 GMT 1500 - 0200|
 |                      .ooo0        | Phone: USA +(719) 488-9416           |
 |                      (   )   Oooo.|                                      |
 .-----------------------\ (----(   )---------------------------------------.
                          \_)    ) /
                                (_/ --=====================_112867765==.ALT-- From owner-chemistry@ccl.net Thu Dec 17 23:11:01 2009 From: "Antonio G. Buljan abuljan%x%udec.cl" To: CCL Subject: CCL:G: Frequencies with Gaussian using PBC Message-Id: <-40939-091217201042-27422-xGtLIQT6b/Yr9gJL8XCGEg(a)server.ccl.net> X-Original-From: "Antonio G. Buljan" Date: Thu, 17 Dec 2009 20:10:39 -0500 Sent to CCL by: "Antonio G. Buljan" [abuljan . udec.cl] Dear Folks... I want to calculate the IR and Raman frequencies of a solid state compound (CaTiO3) using Gaussian03 with PBC option. (PBC = periodic boundary conditions). I tried different calculation options, but the program crashed and the error messages are not clear. My question is: It is possible calculate frequencies (IR and Raman) with Gaussian03 using PBC options? All the best, Antonio