From owner-chemistry@ccl.net Fri Jun 22 02:56:00 2012
From: "oguz gurbulak gurbulakoguz#yahoo.com" <owner-chemistry:server.ccl.net>
To: CCL
Subject: CCL: about ccl programs
Message-Id: <-47120-120622025506-32549-4Rv8/p1PN7vBl3MeU3w+/A:server.ccl.net>
X-Original-From: "oguz gurbulak" <gurbulakoguz%yahoo.com>
Date: Fri, 22 Jun 2012 02:55:05 -0400
Sent to CCL by: "oguz gurbulak" [gurbulakoguz..yahoo.com]
Dear Huub,
Thank you very much for the reply. The programs I determined from the www.ccl.net web site are :
631. FCARTP: A Series of Programs Used to Generate a Predicted Set of Fundamental Vibrational Frequencies (most needed)
QCMP132. ARVOMOL: Surface Areas and Volumes of Molecules
QCMP128. ASYM20: A Program for Force Constant and Normal Coordinate Analysis
639. ASYM40: A Program for Force Constant and Normal Coordinate Analysis
640. SIMLYS 2.0: Analysis of Simulation Results.
I want to scale the force field I will use in FCARTP, I want to compute the molecular surface areas and volumes with ARVOMOL, I want to use ASYM20, ASYM40 for normal coordinate analysis and to refine force constants and want to use SIMLYS 2.0 for the analysis of simulation results.
Could you please help me to find these programs for my studies ?
Best regards.
Oguz GURBULAK Ph.D. Student
Ege University Faculty of Science
Department of Physics
Atomic and Molecular Physics
From owner-chemistry@ccl.net Fri Jun 22 04:59:00 2012
From: "Michel Petitjean petitjean.chiral]_[gmail.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: about ccl programs
Message-Id: <-47121-120622041928-2785-+4gZDyeX03a93fLVFd5IAQ-#-server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral{}gmail.com>
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Date: Fri, 22 Jun 2012 10:19:21 +0200
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Sent to CCL by: Michel Petitjean [petitjean.chiral++gmail.com]
Dear Oguz,
You may compute molecular surface areas and volumes with ASV:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
At the difference of most analytical calculations softwares, which
fail when there are more than 3 or sometimes 4 intersecting spheres,
ASV works in the general case.
Practical radii values let to encounter intersections of 6-8 spheres.
When neglecting high order intersections, the error on volumes is
important and the error on surfaces is enormous.
In addition to the analytical calculation, the Monte-Carlo
computations of surfaces and volumes are available in ASV, too.
I cannot help you about the other programmes you requested.
Best regards,
Michel.
Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral:+:gmail.com (preferred),
michel.petitjean:+:univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html
2012/6/22 oguz gurbulak gurbulakoguz#yahoo.com <owner-chemistry:+:ccl.net>:
>
> Sent to CCL by: "oguz �gurbulak" [gurbulakoguz..yahoo.com]
> Dear Huub,
>
> Thank you very much for the reply. The programs I determined from the www.ccl.net web site are :
>
> 631. FCARTP: A Series of Programs Used to Generate a Predicted Set of Fundamental Vibrational Frequencies (most needed)
>
> QCMP132. ARVOMOL: Surface Areas and Volumes of Molecules
>
> QCMP128. ASYM20: A Program for Force Constant and Normal Coordinate Analysis
>
> 639. ASYM40: A Program for Force Constant and Normal Coordinate Analysis
>
> 640. SIMLYS 2.0: Analysis of Simulation Results.
>
>
> I want to scale the force field I will use in FCARTP, I want to compute the molecular surface areas and volumes with ARVOMOL, I want to use ASYM20, ASYM40 for normal coordinate analysis and to refine force constants and want to use SIMLYS 2.0 for the analysis of simulation results.
>
> Could you please help me to find these programs for my studies ?
>
> Best regards.
>
> Oguz GURBULAK Ph.D. Student
> Ege University �Faculty of Science
> Department of Physics
> Atomic and Molecular Physics
>
From owner-chemistry@ccl.net Fri Jun 22 07:40:00 2012
From: "Christina Jenifer msc christinamsc[a]gmail.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate reorganization energy for hole/electron transfer
Message-Id: <-47122-120622010017-31885-ACmfJyx2cosa2xrBDjPePw|-|server.ccl.net>
X-Original-From: "Christina Jenifer msc" <christinamsc%a%gmail.com>
Date: Fri, 22 Jun 2012 01:00:16 -0400
Sent to CCL by: "Christina Jenifer msc" [christinamsc{}gmail.com]
Dear All,
I am doing TDDFT calculation of curtain OLED molecules using Gaussian09 software. I would like to know how to calculate reorganization energy for hole/electron transfer. I have read the following paper J. Phys. Org. Chem. 2009, 22 11041113. They have explained as follows
lamda hole = lamda 0 + lamda + = (E*0-E0)+(E*+-E+)
lamda electron = lamda 0 + lamda - = (E*0-E0)+(E*--E-)
E0 and E+ represent the energies of the neutral and cation species in their lowest energy geometries, respectively, while E*0 and E*+ represent the energies of the neutral and cation species with the geometries of the cation and neutral species, respectively.
It is confusing for me. I have calculated E0 , E+ and E- but I dont know how to calculate E*0 , E*+ and E*-. Please help me. Thanks in advance.
Thanks in advance
With Regards
Christina
From owner-chemistry@ccl.net Fri Jun 22 10:47:00 2012
From: "sanam s dehkordi zsdehkordi00(0)gmail.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: Autodock
Message-Id: <-47123-120622085508-23189-kjJKlInnLsz39nQr1JHhWg|,|server.ccl.net>
X-Original-From: "sanam s dehkordi" <zsdehkordi00:-:gmail.com>
Date: Fri, 22 Jun 2012 08:55:08 -0400
Sent to CCL by: "sanam s dehkordi" [zsdehkordi00*o*gmail.com]
I want help about using Auto-dock software. I have some questions. for example : why must we add polar hydrogen to macromolecules?
From owner-chemistry@ccl.net Fri Jun 22 12:54:00 2012
From: "Sergio Galembeck segalemb.:.usp.br" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate reorganization energy for hole/electron transfer
Message-Id: <-47124-120622113139-6392-lDXCzuH9eHTS4uwcHRyR+A,server.ccl.net>
X-Original-From: Sergio Galembeck <segalemb ~~ usp.br>
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Date: Fri, 22 Jun 2012 12:31:28 -0300
Mime-Version: 1.0 (Apple Message framework v1278)
Sent to CCL by: Sergio Galembeck [segalemb{}usp.br]
Christina,
To calculate E*0 you need to get the geometry optimized for the cation and change the charge and the multiplicity. The charge will be 0. E+* should be calculate using the optimized geometry of the neutral, setting up the charge and the multiplicity.
Hope this help you,
Sergio
On 22/06/2012, at 02:00, Christina Jenifer msc christinamsc[a]gmail.com wrote:
>
> Sent to CCL by: "Christina Jenifer msc" [christinamsc{}gmail.com]
> Dear All,
> I am doing TDDFT calculation of curtain OLED molecules using Gaussian09 software. I would like to know how to calculate reorganization energy for hole/electron transfer. I have read the following paper J. Phys. Org. Chem. 2009, 22 11041113. They have explained as follows
>
> lamda hole = lamda 0 + lamda + = (E*0-E0)+(E*+-E+)
>
> lamda electron = lamda 0 + lamda - = (E*0-E0)+(E*--E-)
>
> E0 and E+ represent the energies of the neutral and cation species in their lowest energy geometries, respectively, while E*0 and E*+ represent the energies of the neutral and cation species with the geometries of the cation and neutral species, respectively.
>
> It is confusing for me. I have calculated E0 , E+ and E- but I dont know how to calculate E*0 , E*+ and E*-. Please help me. Thanks in advance.
>
> Thanks in advance
>
> With Regards
> Christina>
>
>