From owner-chemistry@ccl.net Wed Jan 28 02:15:01 2015 From: "Bjoern Baumeier baumeier*mpip-mainz.mpg.de" To: CCL Subject: CCL:G: Reorganization energy Message-Id: <-50966-150127170606-10980-9I4OrvW01sFjQY0hFNRuaQ : server.ccl.net> X-Original-From: Bjoern Baumeier Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 27 Jan 2015 23:05:54 +0100 MIME-Version: 1.0 Sent to CCL by: Bjoern Baumeier [baumeier^^^mpip-mainz.mpg.de] For that, you might want to have a look at: "Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors" JCTC 7 (10), 3335–3345 (2011) You need to run three geometry optimizations: neutral, anion, cation Then you need to run additionally anion and cation in neutral geometry, neutral molecule in anion and cation geometries. From the total energies of these calculations, you can determine the reorganization energies U according to Eq. 3 as lambda_hole = U(neutral, cation geometry) - U(neutral, neutral geometry) + U(cation, neutral geometry) - U (cation, cation geometry) and accordingly for lambda_electron. On 1/27/15 5:41 PM, Reeta Felscia felsciadavid92__gmail.com wrote: > Sent to CCL by: "Reeta Felscia" [felsciadavid92-x-gmail.com] > Dear everyone, > I m interested in calculating electron and hole mobilities using Gaussian > 03...let me know the procedure to find reorganization energy with cationic and > aninonic form... could you please help me to find....?> > -- Dr. Bjoern Baumeier Max Planck Institute for Polymer Research Ackermannweg 10 - 55128 Mainz - Germany Theory Group (Office 2.107B), Telephone: +49-(0)-6131-379-267 (internal 267) Fax: +49-(0)-6131-379-340 Email: baumeier- -mpip-mainz.mpg.de Web: http://www.mpip-mainz.mpg.de/~baumeier Researcher ID: http://www.researcherid.com/rid/B-7951-2008 From owner-chemistry@ccl.net Wed Jan 28 03:46:01 2015 From: "Ross Walker rcw+/-sdsc.edu" To: CCL Subject: CCL: AMBER MD Workshop Announcement - Haifa Israel, Sun Apr 26th to 30th. Message-Id: <-50967-150128020428-5036-+Yghi6/82995dVNDTnYIqQ||server.ccl.net> X-Original-From: "Ross Walker" Date: Wed, 28 Jan 2015 02:04:27 -0500 Sent to CCL by: "Ross Walker" [rcw]*[sdsc.edu] <<>> Dear All, You are cordially invited to attend an AMBER Molecular Dynamics training workshop to be held at the Technion Institute in Haifa, Israel from Sun April 26th to Thur April 30th 2015. This workshop is being hosted jointly by the Bioinformatics Knowledge Unit of Technion, the AMBER Development Team and NVIDIA Inc. Details and registration information can be found here: http://biology.technion.ac.il/~amber_workshop_technion_israel/ Scope of the workshop: This five day workshop will introduce researchers in the field of molecular simulations to the broad collection of computational toolsimplemented in the AMBER and AmberTools software packages for molecular dynamics (MD) simulations. It will consist of a combination of lectures and hands on tutorials that provide comprehensive introduction to molecular dynamics and molecular simulation focusing on practical application of version 14 of the AMBER MD software. The workshop consists of a series of short lectures followed by hands-on lab sessions that cover the use of AMBER and AmberTools and the theory behind it. There will be opportunities for discussion with thetutors for advice with specific research problems. List of provisional topics: Introduction to force fields and molecular dynamics. Overview of AMBER and AmberTools and its programs. Introduction to setting up and running simulations. Visualizing AMBER simulations. Overview of AMBER Force Fields / Solvent Models etc. Introduction to implicit solvent and binding energy calculations. Protein folding and advanced analysis. Designing good simulation projects. Dealing with non-standard residues. What to do if there is no crystal structure. Statistical mechanics for free energy calculations. QM/MM coupled potential simulations. Advanced sampling methods. Lipid bilayer simulations. GPU accelerated molecular dynamics simulations. All students will receive a USB pen drive which contains all software and materials used in the workshop. Workshop Instructors: Professor Ross Walker (San Diego Supercomputer Center, UC San Diego, USA) Professor Adrian Roitberg (Department of Chemistry, University of Florida, USA) Professor Thomas Cheatham (Department of Pharmacology, University of Utah, USA) Target audience: Attendees are expected to be graduate students and postdocs as well as young lecturerswho have limited experience in molecular dynamics simulations and/or the AMBER and AmberTools software packages and would benefit from an introductory workshop that also covers advanced topics and the latestfeatures in the AMBER software, including GPU acceleration. The workshop will also be of use to those looking to convert from a different MD simulationpackage such as NAMD, CHARMM, Gromacs or Lammps. Dates of workshop: Sunday April 26th to Thursday April 30th 2015 Eligibility and Organization: This workshop is open to everyone. The event is organized by the Technion Institute, thus any questions may be directed to Dr. Fabian Glaser (fglaser{:}technion.ac.il) and not to the invited speakers/tutors. Registration fee: The registration fee, payable at the time of registering, is $200 USD and covers instructional materials including pen drives, refreshments and a workshop dinner. All participants are responsible for their own travel andaccommodation. Please contact Dr. Glaser for payment options. Accommodation: Accommodation at the Technion is possible and will require additional payment. For housing information see: http://www.segeltechnion.org.il/TTFA/Templates/ShowPage.asp? DBID=1&LNGID=2&T%20MID=84&FID=572 Poster Session: Although not mandatory participants are encouraged to bring posters highlighting their work for a poster session that will be held one evening during the workshop. A total of two NVIDIA K40 graphics cards will be given as prize to the best posters. Application deadline: Monday 30th March 2015* *The number of places for this workshop is limited. If there is an unprecedented demand, we may have to restrict the number of people from the same research group. Please note that application may close early if all places have beenfilled before the deadline. Application form: Please visit the following web link for the online application form. http://bku.technion.ac.il/BKU/Templates/showpage.asp? DBID=1&LNGID=1&TMID=100&FID=512&PID=0&IID=2032 Sponsors: NVIDIA, Technion, The Moshe Yanai Fund for the Promotion of international Conferences From owner-chemistry@ccl.net Wed Jan 28 06:07:00 2015 From: "=?UTF-8?Q?Serdar_Bado=C4=9Flu?= serdarbadoglu(a)gmail.com" To: CCL Subject: CCL:G: PBC condition Message-Id: <-50968-150128060534-10937-9Sgg2X4IGwvJqWm9f7XmDA#server.ccl.net> X-Original-From: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= Content-Type: multipart/alternative; boundary=001a11c374b8552e35050db4591a Date: Wed, 28 Jan 2015 13:05:27 +0200 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Serdar_Bado=C4=9Flu?= [serdarbadoglu[]gmail.com] --001a11c374b8552e35050db4591a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Even you can define the translation vector correctly your PBC calculations may fail again wihout any apparent reason. Unfortunately, PBC calculation is the soft point of Gaussian software. Good luck with your issue. On Tue, Jan 27, 2015 at 6:16 PM, Marc Raupach raupach%% students.uni-marburg.de wrote: > As far as I understand the Gaussian manual the only thing you have to ad= d > are the translation vectors at the end of the molecule specification. (wi= th > no intervening blank line) > > For example a two dimensional pbc calculation: > [...] > > 0 1 > C 0.000000 0.000000 0.000000 > C 0.000000 1.429118 0.000000 > TV 2.475315 0.000000 0.000000 > TV -1.219952 2.133447 0.000000 > > [...] > > Since you have not shown your xyz-block I can only speculate that you > might have done something wrong at that point. > > Greetings, > Marc > > Am 27.01.2015 um 12:40 schrieb Partha Sengupta anapspsmo~~gmail.com: > > I am using Gaussian 09w Revision C.01. > > #p HSEh1PBE/Gen pseudo=3Dread opt Int(Grid=3DUltraFine) Pop=3DRegular > FMM=3D(print) > > IOp1=3Dtimestamp IOp(5/13=3D1,5/33=3D1) > > SCF=3D(NoVarAcc,NoIncFock,Tight) > > > > Charge multiplicity > > X Y Z > > =E2=80=A6=E2=80=A6. > > o h s 0 > > 6-31g(d) > > **** > > zn 0 > > lanl2dz > > **** > > > > zn 0 > > lanl2dz > > > > at the end > > the end is > Leave Link 303 at Tue Jan 27 17:01:53 2015, MaxMem=3D 183500800 cpu: > 11.0 > (Enter C:\G09W\l401.exe) > Top of link 401. Tue Jan 27 17:01:54 2015 0.00 cpu seconds. > After setup. Tue Jan 27 17:01:54 2015 0.00 cpu seconds. > Harris functional with IExCor=3D 1009 diagonalized for initial guess. > Top of HarFok. Tue Jan 27 17:01:54 2015 0.00 cpu seconds. > RepCel: MaxNCR=3D 571 NClRep=3D 571 NMtPBC=3D 571. > HarFok: IExCor=3D 1009 AccDes=3D 0.00D+00 IRadAn=3D 5 IDoV=3D 2 > ScaDFX=3D 1.000000 1.000000 1.000000 1.000000 > Top of CalDSu Tue Jan 27 17:01:54 2015 0.00 cpu seconds. > Dimensions of /B2/ exceeded in AtP2B2. > Error termination via Lnk1e in C:\G09W\l401.exe at Tue Jan 27 17:01:54 > 2015. > Job cpu time: 0 days 0 hours 1 minutes 15.0 seconds. > File lengths (MBytes): RWF=3D 675 Int=3D 0 D2E=3D 0 Chk=3D= 1 > Scr=3D 1 > > > > On Tue, Jan 27, 2015 at 5:05 PM, Partha Sengupta > wrote: > >> I am using Gaussian 09w Revision C.01. >> >> the input/Route section >> #p HSEh1PBE/Gen pseudo=3Dread opt Int(Grid=3DUltraFine) Pop=3DRegular >> FMM=3D(print) >> IOp1=3Dtimestamp IOp(5/13=3D1,5/33=3D1) >> SCF=3D(NoVarAcc,NoIncFock,Tight) >> >> the end is >> Leave Link 303 at Tue Jan 27 17:01:53 2015, MaxMem=3D 183500800 >> cpu: 11.0 >> (Enter C:\G09W\l401.exe) >> Top of link 401. Tue Jan 27 17:01:54 2015 0.00 cpu seconds. >> After setup. Tue Jan 27 17:01:54 2015 0.00 cpu seconds. >> Harris functional with IExCor=3D 1009 diagonalized for initial guess. >> Top of HarFok. Tue Jan 27 17:01:54 2015 0.00 cpu seconds. >> RepCel: MaxNCR=3D 571 NClRep=3D 571 NMtPBC=3D 571. >> HarFok: IExCor=3D 1009 AccDes=3D 0.00D+00 IRadAn=3D 5 IDoV=3D = 2 >> ScaDFX=3D 1.000000 1.000000 1.000000 1.000000 >> Top of CalDSu Tue Jan 27 17:01:54 2015 0.00 cpu seconds. >> Dimensions of /B2/ exceeded in AtP2B2. >> Error termination via Lnk1e in C:\G09W\l401.exe at Tue Jan 27 17:01:54 >> 2015. >> Job cpu time: 0 days 0 hours 1 minutes 15.0 seconds. >> File lengths (MBytes): RWF=3D 675 Int=3D 0 D2E=3D 0 Chk= =3D 1 >> Scr=3D 1 >> >> >> On Tue, Jan 27, 2015 at 1:22 PM, Marc Raupach raupach_._ >> students.uni-marburg.de wrote: >> >>> >>> Sent to CCL by: Marc Raupach [raupach+/-students.uni-marburg.de] >>> Hi, >>> >>> you have to tell us at least the name of the program package, the >>> program version and the output file which contains the error message! >>> >>> Greetings, >>> Marc >>> Am 27.01.2015 um 05:46 schrieb Partha Sengupta anapspsmo a gmail.com: >>> >>> Friends, I want to do a optimization in Periodic Boundary condition >>>> calculation (PBC) for a system containing S and Zn. But it fails. Plea= se >>>> tell me route section so that I can do the work >>>> >>>> -- >>>> Dr. Partha Sarathi Sengupta >>>> Associate Professor >>>> Vivekananda Mahavidyalaya, Burdwan >>>> >>> >>> >>> >>> >>> E-mail to subscribers: CHEMISTRY---ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST---ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtm= lConferences: >>> http://server.ccl.net/chemistry/announcements/conferences/>>> >>> >>> >> >> >> -- >> Dr. Partha Sarathi Sengupta >> Associate Professor >> Vivekananda Mahavidyalaya, Burdwan >> > > > > -- > Dr. Partha Sarathi Sengupta > Associate Professor > Vivekananda Mahavidyalaya, Burdwan > > > --=20 Serdar BADO=C4=9ELU, Ph.D. Gazi =C3=9Cniversitesi Fizik B=C3=B6l=C3=BCm=C3=BC --001a11c374b8552e35050db4591a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Even you can define the translation vector correctly your = PBC calculations may fail again wihout any apparent reason. Unfortunately, = PBC calculation is the soft point of Gaussian software. Good luck with your= issue.

On T= ue, Jan 27, 2015 at 6:16 PM, Marc Raupach raupach%%students.uni-marburg.de <owner-chemistry],[ccl.= net> wrote:
=20 =20 =20
As far as I understand the Gaussian manual the only thing you have to add are the translation vectors at the end of the molecule specification. (with no intervening blank line)

For example a two dimensional pbc calculation:
[...]
0 1
C                  0.000000    0.000000    0.000000
C                  0.000000    1.429118    0.000000
TV                 2.475315    0.000000    0.000000
TV                -1.219952    2.133447    0.000000
[...]

Since you have not shown your xyz-block I can only speculate that you might have done something wrong at that point.

Greetings,
Marc

Am 27.01.2015 um 12:40 schrieb Partha Sengupta anapspsmo~~gm= ail.com:

I am using Gaussian 09w Revision C.01.

#p HSEh1PBE/Gen pseudo=3Dread opt=C2=A0 Int(Grid=3DUltraFine) Pop=3DRegular FMM=3D(print)=

IOp1=3Dtimestamp IOp(5/13=3D1,5/33=3D1)

SCF=3D(NoVarAcc,NoIncFock,Tight)

=C2=A0

Charge multiplicity

X =C2=A0Y Z

=E2=80=A6=E2=80=A6.

o h s 0

6-31g(d)

****

zn 0

lanl2dz

****

=C2=A0

zn 0

lanl2dz

=C2=A0

at the end

the end is
=C2=A0Leave Link=C2=A0 303 at Tue Jan 27 17:01:53 2015, MaxMem=3D= =C2=A0 183500800 cpu:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 11.0
=C2=A0(Enter C:\G09W\l401.exe)
=C2=A0Top of link=C2=A0 401.=C2=A0=C2=A0=C2=A0 Tue Jan 27 17:01:5= 4 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 cpu seconds.<= br> =C2=A0After setup.=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 Tue Jan 27 17:01:54 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 cpu = seconds.
=C2=A0Harris functional with IExCor=3D 1009 diagonalized for init= ial guess.
=C2=A0Top of HarFok.=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tue Jan = 27 17:01:54 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 cpu seconds.<= br> =C2=A0RepCel:=C2=A0 MaxNCR=3D=C2=A0=C2=A0=C2=A0=C2=A0 571 NClRep=3D=C2=A0=C2=A0=C2=A0=C2=A0 571 NMtPBC=3D=C2=A0=C2=A0=C2=A0= =C2=A0 571.
=C2=A0HarFok:=C2=A0 IExCor=3D 1009 AccDes=3D 0.00D+00 IRadAn=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 5 IDoV= =3D 2
=C2=A0ScaDFX=3D=C2=A0 1.000000=C2=A0 1.000000=C2=A0 1.000000=C2= =A0 1.000000
=C2=A0Top of CalDSu=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tue= Jan 27 17:01:54 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 cpu = seconds.
=C2=A0Dimensions of /B2/ exceeded in AtP2B2.
=C2=A0Error termination via Lnk1e in C:\G09W\l401.exe at Tue Jan = 27 17:01:54 2015.
=C2=A0Job cpu time:=C2=A0 0 days=C2=A0 0 hours=C2=A0 1 minutes 15= .0 seconds.
=C2=A0File lengths (MBytes):=C2=A0 RWF=3D=C2=A0=C2=A0=C2=A0 675 Int=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0 D2E=3D=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 0 Chk=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1 Scr=3D=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0 1

=C2=A0


On Tue, Jan 27, 2015 at 5:05 PM, Partha Sengupta <anapspsmo---gmail.com> wrote:
I am using Gaussian 09w Revision C.01.

the input/Route section
#p HSEh1PBE/Gen pseudo=3Dread opt=C2=A0 Int(Grid=3DUltraFin= e) Pop=3DRegular FMM=3D(print)
IOp1=3Dtimestamp IOp(5/13=3D1,5/33=3D1)
SCF=3D(NoVarAcc,NoIncFock,Tight)

the end is
=C2=A0Leave Link=C2=A0 303 at Tue Jan 27 17:01:53 2015, MaxMe= m=3D=C2=A0 183500800 cpu:=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 11.0
=C2=A0(Enter C:\G09W\l401.exe)
=C2=A0Top of link=C2=A0 401.=C2=A0=C2=A0=C2=A0 Tue Jan 27 17:= 01:54 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 cpu seconds.
=C2=A0After setup.=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0 Tue Jan 27 17:01:54 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0= .00 cpu seconds.
=C2=A0Harris functional with IExCor=3D 1009 diagonalized for initial guess.
=C2=A0Top of HarFok.=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tue = Jan 27 17:01:54 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 cpu seconds.
=C2=A0RepCel:=C2=A0 MaxNCR=3D=C2=A0=C2=A0=C2=A0=C2=A0 571 NCl= Rep=3D=C2=A0=C2=A0=C2=A0=C2=A0 571 NMtPBC=3D=C2=A0=C2=A0=C2=A0=C2=A0 571. =C2=A0HarFok:=C2=A0 IExCor=3D 1009 AccDes=3D 0.00D+00 IRadAn= =3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 5 IDoV=3D 2
=C2=A0ScaDFX=3D=C2=A0 1.000000=C2=A0 1.000000=C2=A0 1.000000= =C2=A0 1.000000
=C2=A0Top of CalDSu=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= Tue Jan 27 17:01:54 2015=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0.00 cpu seconds.
=C2=A0Dimensions of /B2/ exceeded in AtP2B2.
=C2=A0Error termination via Lnk1e in C:\G09W\l401.exe at Tue Jan 27 17:01:54 2015.
=C2=A0Job cpu time:=C2=A0 0 days=C2=A0 0 hours=C2=A0 1 minute= s 15.0 seconds.
=C2=A0File lengths (MBytes):=C2=A0 RWF=3D=C2=A0=C2=A0=C2=A0 6= 75 Int=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 0 D2E=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0 0 Chk=3D=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1 Scr=3D=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0 1


On Tue, Jan 27, 2015 at 1:22 PM, Marc Raupach raupach_._students.uni-marburg.de <owne= r-chemistry---ccl.net> wrote:

Sent to CCL by: Marc Raupach [raupach+/-students.uni-marburg.de= ]
Hi,

you have to tell us at least the name of the program package, the program version and the output file which contains the error message!

Greetings,
Marc
Am 27.01.2015 um 05:46 schrieb Partha Sengupta anapspsmo a gmail.com:

Friends, I want to do a optimization in Periodic Boundary condition calculation (PBC) for a system containing S and Zn. But it fails. Please tell me route section so that I can do the work

--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan




E-mail to subscribers: CHEMISTRY---ccl.net or use:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/c= cl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST---ccl.net or use
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/c= cl/send_ccl_message

Subscribe/Unsubscribe:=C2=A0 =C2=A0 =C2=A0 http://= www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/ch= emistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry= /searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutcc= l/instructions/





--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan



--
Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan




--
Serdar BADO=C4=9ELU, Ph.D.
Gazi =C3=9Cniversitesi F= izik B=C3=B6l=C3=BCm=C3=BC
--001a11c374b8552e35050db4591a-- From owner-chemistry@ccl.net Wed Jan 28 07:29:01 2015 From: "Niveditha reddy s nivs916 a gmail.com" To: CCL Subject: CCL: calculation of transitionstate Message-Id: <-50969-150128072737-13725-r3AiRm4MFdn8CpDTvPF7/Q#server.ccl.net> X-Original-From: "Niveditha reddy s" Date: Wed, 28 Jan 2015 07:27:32 -0500 Sent to CCL by: "Niveditha reddy s" [nivs916::gmail.com] Dear all, greetings, I'm performing a calculation of transition states for a free radical chain reaction (self accelerating reaction) . The chain reaction consists of 8 steps. i have calculated transition states for 6 steps using QST3 method in G09. But Im not able to find the transition states for 1st and 8th steps. These two steps are of high activation energy, according to the literature. The first step (initialization reaction) is about breaking a peroxide bond of an aromatic hydroperoxide, thus forming a hydroxyl radical and aryloxy radical. Second step is release of methyl radical from the aryloxy radical so as to produce a stable closed shell product. Second step is a exothermic reaction with very less activation energy (6 kj/mol). The aromatic hydroperoxide has six rotamers, and this is creating problem in finding the transition state. whatever initial guess Im providing, most of the time output is a transition state regarding the conversion of one rotamer to another. I have also tried relaxed potential energy surface scan of peroxy bond and took initial guess from this for qst3. Then the resulting transition state is about release of a methyl radical along with hydroxyl radical. I tried freezing the bonds, but could not get the required transition state. So my questions are: 1) Is the transition state for first step is very week, and thats why im not able to find it? 2) Is low activation energy, and high exothermicity of second step reason for why Im not able to find the transition state for first step? can any one clarify my doubts and sujjest me what to do??? Any help would be greatly appreciated. Thanks in advance. From owner-chemistry@ccl.net Wed Jan 28 22:38:01 2015 From: "Reeta Felscia felsciadavidphy=gmail.com" To: CCL Subject: CCL:G: Reorganization energy Message-Id: <-50970-150128090623-4370-hCEkx9UeJ+2uGKpOf6NoUA]-[server.ccl.net> X-Original-From: Reeta Felscia Content-Type: multipart/alternative; boundary=047d7b87501cffcbe9050db6df6e Date: Wed, 28 Jan 2015 19:36:16 +0530 MIME-Version: 1.0 Sent to CCL by: Reeta Felscia [felsciadavidphy!=!gmail.com] --047d7b87501cffcbe9050db6df6e Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Thank you sir.. It is useful for me to calculate Reorganization energy... Now I m struck with calculating electron transfer integral V (solving Fock operator) using direct method.... I m using Gaussian 03 software.... On Wed, Jan 28, 2015 at 3:35 AM, Bjoern Baumeier baumeier*mpip-mainz.mpg.de wrote: > > Sent to CCL by: Bjoern Baumeier [baumeier^^^mpip-mainz.mpg.de] > For that, you might want to have a look at: > > "Microscopic Simulations of Charge Transport in Disordered Organic > Semiconductors" JCTC 7 (10), 3335=E2=80=933345 (2011) > > You need to run three geometry optimizations: neutral, anion, cation > Then you need to run additionally anion and cation in neutral geometry, > neutral molecule in anion and cation geometries. > > From the total energies of these calculations, you can determine the > reorganization energies U according to Eq. 3 as > > lambda_hole =3D U(neutral, cation geometry) - U(neutral, neutral geometry= ) + > U(cation, neutral geometry) - U (cation, cation geometry) > > and accordingly for lambda_electron. > > On 1/27/15 5:41 PM, Reeta Felscia felsciadavid92__gmail.com wrote: > >> Sent to CCL by: "Reeta Felscia" [felsciadavid92-x-gmail.com] >> Dear everyone, >> I m interested in calculating electron and hole mobilities using >> Gaussian >> 03...let me know the procedure to find reorganization energy with >> cationic and >> aninonic form... could you please help me to find....?> >> >> > -- > Dr. Bjoern Baumeier > Max Planck Institute for Polymer Research > Ackermannweg 10 - 55128 Mainz - Germany > Theory Group (Office 2.107B), > Telephone: +49-(0)-6131-379-267 (internal 267) > Fax: +49-(0)-6131-379-340 > Email: baumeier-x-mpip-mainz.mpg.de > Web: http://www.mpip-mainz.mpg.de/~baumeier > Researcher ID: http://www.researcherid.com/rid/B-7951-2008 > > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: http://server.ccl.net/ > chemistry/announcements/conferences/> > > --047d7b87501cffcbe9050db6df6e Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Thank you sir.. It is useful for me to calculate Reorganiz= ation energy... Now I m struck with calculating electron transfer integral = V (solving Fock operator) =C2=A0using direct method.... I m using Gaussian = 03 software....

On Wed, Jan 28, 2015 at 3:35 AM, Bjoern Baumeier baumeier*mpip-mainz.mpg.de <owner-chemistry|a|ccl.n= et> wrote:

Sent to CCL by: Bjoern Baumeier [baumeier^^^mpip-mainz.mpg.de]
For that, you might want to have a look at:

"Microscopic Simulations of Charge Transport in Disordered Organic Sem= iconductors" JCTC 7 (10), 3335=E2=80=933345 (2011)

You need to run three geometry optimizations: neutral, anion, cation
Then you need to run additionally anion and cation in neutral geometry, neu= tral molecule in anion and cation geometries.

> From the total energies of these calculations, you can determine the reorga= nization energies U according to Eq. 3 as

lambda_hole =3D U(neutral, cation geometry) - U(neutral, neutral geometry) = + U(cation, neutral geometry) - U (cation, cation geometry)

and accordingly for lambda_electron.

On 1/27/15 5:41 PM, Reeta Felscia felsciadavid92__gmail.com wrote:
Sent to CCL by: "Reeta=C2=A0 Felscia" [felsciadavid92-x-gmail.com]
Dear everyone,
=C2=A0 =C2=A0 =C2=A0I m interested in calculating electron and hole mobilit= ies using Gaussian
03...let me know the procedure to find reorganization energy with cationic = and
aninonic form... could you please help me to find....?>


 --
Dr. Bjoern Baumeier
Max Planck Institute for Polymer Research
Ackermannweg 10 - 55128 Mainz - Germany
Theory Group (Office 2.107B),
Telephone: +49-(0)-6131-379-267=C2=A0 (internal 267)
Fax: +49-(0)-6131-379-340
Email: ba= umeier-x-mpip-mainz.mpg.de
Web: h= ttp://www.mpip-mainz.mpg.de/~baumeier
Researcher ID: http://www.researcherid.com/rid/B-7951-2008=




-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY|a|ccl.net or use:
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= ge

E-mail to administrators: CHEMISTRY-REQUEST|a|ccl.net or use
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_messa= ge

Subscribe/Unsubscribe:=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/= sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.= shtml
=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/=



--047d7b87501cffcbe9050db6df6e--