> > > --f46d0442820e0f18f104c653eeca Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable macmolplt is pretty good too

On 3 August 2012 02:09, Andrew Yeung andrew.yeung/./chem.tamu.edu <owner-chemistry(a)ccl.net>= ; wrote:

Sent to CCL by: Andrew Yeung [andrew.yeung(!)chem.tamu.edu]
With Gaussian, my favorite so far has been Avogadro. This program accepts G= amess too, I believe.

Avogadro crashes every now and then, but when it works, it's wonderful.= If the basis set is printed, it can generate MOs from log files instead of= fchk files.

It creates nice pictures when you export it to POV-Ray, and it cleans up th= e POV-Ray files if you ask it to. It is also able to generate vector graphi= cs in the form of pdf, svg, & eps.

Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837

On 2012-08-02 4:11 AM, AMBAR BANERJEE ambarpchem^gmail.com wrote:

Sent to CCL by: "AMBAR =A0BANERJEE" [ambarpchem....gmail.com]

i was using GAMESS-(US) to do some rhf calculations. i need to visualize th= e MO's using some freely available graphical interface. please help me.= is it possible to generate gaussian cube files from gamess dat files?><= br>

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--f46d0442820e0f18f104c653eeca-- From owner-chemistry@ccl.net Fri Aug 3 03:07:00 2012 From: "psavita savita.pundlik%crl-global.com" To: CCL Subject: CCL: solid state TDDFT Message-Id: <-47309-120803021834-10460-GGoKle6ScL/KW7ArZtvDRA++server.ccl.net> X-Original-From: psavita Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Fri, 3 Aug 2012 11:48:26 +0530 MIME-Version: 1.0 Sent to CCL by: psavita [savita.pundlik(-)crl-global.com] Hello,

You can use Quantum Espresso for solid state TDDFT. To= represent adsorbed species, you may have to use a large unit cell
which= will be highly compute intensive.

Best wishes,

<= div>Savita Pundlik
Compu= tational Materials Research &a= mp; Innovation Group
Computational Research Laboratories= Ltd.,
Taco House, Damle Path, Off Law Co= llege Road
Pune - 411= 004, India.

-----owner-chemistry+savita.pundlik=3D=3Dcrl-global.co= m::ccl.net wrote: -----

T= o: "Pundlik, Savita Sunil " <savita.pundlik::crl-global.com= >
From: "Jonas Baltrusaitis jasius=5F1[-]yahoo.com"
Sent by: owner-chemis= try+savita.pundlik=3D=3Dcrl-global.com::ccl.net
Date: 08/03/2012 08:0= 5AM
Subject: CCL: solid state TDDFT

Sent to CCL by: "Jonas Baltrusaitis" = [jasius=5F1=3D=3D=3Dyahoo.com]
Dear all,

anybody know of software= packages that would be able to perform solid state TDDFT in any form, e.g.= I am interested in surface slab+adsorbed molecule TDDFT optimization. Prob= ably, there is much more to this question since that involves performing an= y element (metal, for example) TDDFT which is probably superhard to do but = I figure I would give it a chance and ask

thanks

Jonas Baltru= saitis
university of Iowa

-=3D This is automatically adde= d to each message by the mailing script =3D-
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= From owner-chemistry@ccl.net Fri Aug 3 09:14:01 2012 From: "psavita savita.pundlik:_:crl-global.com" To: CCL Subject: CCL: Problem in running the post processing code for proline in Quantum Espresso Message-Id: <-47310-120803021545-10290-R0KHU4pzMwOlgk/OYlGfDA_-_server.ccl.net> X-Original-From: psavita Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Fri, 3 Aug 2012 11:45:30 +0530 MIME-Version: 1.0 Sent to CCL by: psavita [savita.pundlik],[crl-global.com] Hi Sabdhya,

Apparently, there is nothing wrong with yo= ur input file. You should get charge density data with this.
One thing I= did not understand, why do you have to do nscf, you may directly go for po= st-processing
after scf. May be that is reason for error.

Good lu= ck,

Savita Pun= dlik
<= span style=3D"font-family: Georgia,Default Serif,serif;">Computational Materials Research & Innovation Group
Computational Res= earch Laboratories Ltd.,
Taco House, Daml= e Path, Off Law College Road
Pune - 411004, India.

=

-----owner-chemistry+savita.pundlik= =3D=3Dcrl-global.com:+:ccl.net wrote: -----

To: "Pundlik, Savita Sunil " <savita.pundl= ik:+:crl-global.com>
From: "Sandhya Rai sandhyachemistry30##gmail.c= om"
Sent by: owner-chemistry+savita.pundlik=3D=3Dcrl-global.com:+:ccl.net
Date= : 08/02/2012 09:49PM
Subject: CCL: Problem in running the post processin= g code for proline in Quantum Espresso

Dear All,

= I am a new user of Quantum Espresso. I am trying to plot the charge density= of proline after performing the 'scf' and 'nscf' calculations.

B= ut I am getting the following error:

=0D=0D=0D

Program POST-PROC v.4.3.2 starts on 2Aug2012 at 18= :25:55

This program is part of= the open-source Quantum ESPRESSO suite

for q= uantum simulation of materials; please cite

=0D=0D=0D

= ; "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395= 502 (2009);

URL http://www.quantum-espres= so.org",

in publications or presentations= arising from this work. More details at

=0D=0D=0D

&= nbsp;http://www.quantum-espresso.org/wiki/ind= ex.php/Citing=5FQuantum-ESPRESSO

= Parallel version (MPI), running on 4 processors

= =0D=0D=0D

R & G space division: proc/pool= =3D 4

Message from routine r= ead=5Ffile:

file /home1/supriya/Quantu= m=5Fespresso=5Fproline/tmp/proline=5Fscf.save not guaranteed to be safe for= post-processing

=0D=0D=0D

The input = file that I am giving is:

&INPUTPP

&nb= sp; prefix = =3D 'proline=5Fscf' ,

&= nbsp; outdir =3D '/home1/supriya/Quantum=5Fespr= esso=5Fproline/tmp' ,

=0D=0D

&n= bsp; filplot =3D 'prolinecharge' ,

<= div> p= lot=5Fnum =3D 0,

= spin=5Fcomponent =3D 0 ,

&PLOT

= nfile =3D 1 ,

=0D=0D

&nbs= p; filepp(1) =3D 'prolinecharge',

wei= ght(1) =3D 1.0,

= fileout =3D 'proline.pp.gnu' ,

= = ;iflag =3D 2 ,

=0D=0D

&n= bsp; output=5Fformat =3D 0 ,

&n= bsp; e1(1) =3D 1.0,

&n= bsp; e1(2) =3D 0.0,

&nbs= p; e1(3) =3D 0.0,

= &nbs= p;e2(1) =3D 0.0,

=0D=0D

= e2(2) =3D 0.0,

&n= bsp; e= 2(3) =3D 1.0,

&n= bsp; nx =3D 56 ,

= &nbs= p; ny =3D 40 ,

=0D=0D

<= div> &= nbsp; = &nbs= p;

--
San= dhya Rai
Pursuing Ph.D
Centre of Computational Natural Sciences &= Bioinformatics
=0DInternational Institute of Information & Technolo= gy
Gachibowli, Hyderabad.

=0D=0D<= /div>= From owner-chemistry@ccl.net Fri Aug 3 09:49:00 2012 From: "mwishway linkon meishwaylinkon]^[yahoo.com" To: CCL Subject: CCL: electrostatic potential surface MEP Message-Id: <-47311-120803042601-6271-sF/Z4oayBIqknzUNeK1vzg ~~ server.ccl.net> X-Original-From: "mwishway linkon" Date: Fri, 3 Aug 2012 04:25:56 -0400 Sent to CCL by: "mwishway linkon" [meishwaylinkon_+_yahoo.com] HELLO EVERYBODY ! Can anyone guide me about electrostatic potential surface MEP ,i know how to draw it but after it i don't know , why just one color appear over whole molecule , like mine is a X shape big molecule ,also the values appear over the scale bar what do they represent , how i can change color if i want to show positive , negative density color over the diagram . please help me as am totally confused about this MEP. From owner-chemistry@ccl.net Fri Aug 3 10:24:00 2012 From: "meishway linkon meishwaylinkon*_*yahoo.com" To: CCL Subject: CCL: %age composition of fragments Message-Id: <-47312-120803043147-7181-rpfo0i6oGUDjiletMQWm9A.:.server.ccl.net> X-Original-From: "meishway linkon" Date: Fri, 3 Aug 2012 04:31:45 -0400 Sent to CCL by: "meishway linkon" [meishwaylinkon]|[yahoo.com] Hello ! can someone tell me how to calculate %age composition of donor and acceptor fragements for a donor molecules, e.g. if there is a donor X , it has two donor fragment a, b and one acceptor fragemen c , then how i will calculate that HOMO of X donor have how much contribution from a, b and c . From owner-chemistry@ccl.net Fri Aug 3 10:58:01 2012 From: "Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com" To: CCL Subject: CCL: Negative Barrier Height Message-Id: <-47313-120803100554-2790-q7bE1r+KtjrN1hYXltcRvg=-=server.ccl.net> X-Original-From: "Dr. Bhupesh Kumar Mishra" Date: Fri, 3 Aug 2012 10:05:51 -0400 Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffmail.com] Dear All, I am doing some calculation on reaction mechanism. I have optimized transition states. But the problem is that it is characterized by low vibrational frequency (<100 cm-1). The calculated barrier heights are negative. Whether it is possible? May negative barrier heights for TS are acceptable for understanding of any reaction mechanism? Any suggestions is highly appreciated. Sincerely Bhupesh Kumar Mishra(Ph.D.) UGC-Dr. D. S. Kothari Post Doctoral Fellow Department of Chemical Sciences Tezpur University Tezpur- ASSAM INDIA From owner-chemistry@ccl.net Fri Aug 3 11:43:01 2012 From: "Luke Crawford luke.crawford.437=gmail.com" To: CCL Subject: CCL: Negative Barrier Height Message-Id: <-47314-120803113742-16678-wNGWW76mOpvkzWNGaAVLbA:-:server.ccl.net> X-Original-From: Luke Crawford Content-Type: multipart/alternative; boundary="501bf03b_61574095_a879" Date: Fri, 3 Aug 2012 16:37:31 +0100 MIME-Version: 1.0 Sent to CCL by: Luke Crawford [luke.crawford.437[A]gmail.com] --501bf03b_61574095_a879 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi Bhupesh, Are the energies which are lower than your reactants the electronic, enthalpic or free energies? Are you taking the values against separated reactant species and if so, could some sort of complex exist prior to approaching the transition state that could potentially be lower than separated reactants? Is the reaction you are modelling one which occurs in solution? If so, you may need to account for this somehow, perhaps using single points of the gas phase geometries with a PCM model or such like. This could have an impact upon relative energies. Not sure if that helps too much (you may have already considered these effects) but some quick and easy things to look into if you haven't. Thanks, Luke Crawford School of Chemistry, University of St. Andrews, Fife, Scotland On Friday, 3 August 2012 at 15:05, Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com wrote: > > Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffmail.com (http://bhupesh_chem__rediffmail.com)] > Dear All, > I am doing some calculation on reaction mechanism. I have optimized transition states. But the problem is that it is characterized by low vibrational frequency (<100 cm-1). The calculated barrier heights are negative. Whether it is possible? May negative barrier heights for TS are acceptable for understanding of any reaction mechanism? > Any suggestions is highly appreciated. > > Sincerely > Bhupesh Kumar Mishra(Ph.D.) > UGC-Dr. D. S. Kothari Post Doctoral Fellow > Department of Chemical Sciences > Tezpur University > Tezpur- ASSAM > INDIA> > E-mail to subscribers: CHEMISTRY]^[ccl.net (mailto:CHEMISTRY]^[ccl.net) or use:> > E-mail to administrators: CHEMISTRY-REQUEST]^[ccl.net (mailto:CHEMISTRY-REQUEST]^[ccl.net) or use--501bf03b_61574095_a879 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

Hi Bhupesh,

Are the energies which are lowe= r than your reactants the electronic, enthalpic or free energies=3F Are y= ou taking the values against separated reactant species and if so, could = some sort of complex exist prior to approaching the transition state that= could potentially be lower than separated reactants=3F

<= br>

Is the reaction you are modelling one which occurs in solut= ion=3F If so, you may need to account for this somehow, perhaps using sin= gle points of the gas phase geometries with a PCM model or such like. Thi= s could have an impact upon relative energies.

N= ot sure if that helps too much (you may have already considered these eff= ects) but some quick and easy things to look into if you haven't.

Thanks,

Luke Crawford

School of Chemistry,

University of St. Andrews,

=46= ife,

Scotland

=20

On =46riday, 3 August = 2012 at 15:05, Dr. Bhupesh Kumar Mishra bhupesh=5Fchem(=5F)rediffmail.com= wrote:

Sent to CCL by: =22= Dr. Bhupesh Kumar Mishra=22 =5Bbhupesh=5Fchem=5F=5Frediffmail.com=5D
Dear = All,
I am doing some calculation on reaction mechanism. I have = optimized transition states. But the problem is that it is characterized = by low vibrational frequency (<100 cm-1). The calculated barrier heigh= ts are negative. Whether it is possible=3F May negative barrier heights f= or TS are acceptable for understanding of any reaction mechanism=3F
=
Any suggestions is highly appreciated.

Sin= cerely
Bhupesh Kumar Mishra(Ph.D.)
UGC-Dr. D. S. Kot= hari Post Doctoral =46ellow
Department of Chemical Sciences
Tezpur University
Tezpur- ASSAM
INDIA

-=3D This is automatically= added to each message by the mailing script =3D-
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the= strange characters on the top line to the =40 sign. You can also
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--501bf03b_61574095_a879-- From owner-chemistry@ccl.net Fri Aug 3 14:06:00 2012 From: "cina foroutan canyslopus#%#yahoo.co.uk" To: CCL Subject: CCL: Negative Barrier Height Message-Id: <-47315-120803123541-29274-cvVUcXUZO/34WaMbA+9/TQ]_[server.ccl.net> X-Original-From: cina foroutan Content-Type: multipart/alternative; boundary="435439028-1490379958-1344011729=:78868" Date: Fri, 3 Aug 2012 17:35:29 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: cina foroutan [canyslopus]![yahoo.co.uk] --435439028-1490379958-1344011729=:78868 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Dr. Kumar,=0A=0AWhat that you found barely is not a TS. It is a comple= x between reactant and product (if you are studying a 2 component reaction)= . Many reactions in gas phase or in absence of solvent molecules has no rea= l barrier. For instance the well-known SN1 reaction in absence of solvent m= olecules has just one TS since the second TS, which can be found in all tex= t books, is due to solvent reorganization around Nu and carbocation.=0AI am= not aware of the reaction that you are studying but this reaction might be= of a similar class of reactions. Be careful about interpretation of reacti= on mechanism in gas phase and absence of solvent molecules.=0A=0ABest wishe= s,=0ACina=0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=0ACina Foroutan-Nejad, Ph.D.=0Ahttp://independent.academ= ia.edu/CinaForoutanNejad=0A=0A=0A=0A________________________________=0A Fro= m: Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com =0ATo: "Foroutan-Nejad, Cina " =0A= Sent: Friday, 3 August 2012, 17:35=0ASubject: CCL: Negative Barrier Height= =0A =0A=0ASent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffm= ail.com]=0ADear All,=0AI am doing some calculation on reaction mechanism. I= have optimized transition states. But the problem is that it is characteri= zed by low vibrational frequency (<100 cm-1). The calculated barrier height= s are negative. Whether it is possible? May negative barrier heights for TS= are acceptable for understanding of any reaction mechanism?=0AAny suggesti= ons is highly appreciated.=0A=0ASincerely=0ABhupesh=A0 Kumar Mishra(Ph.D.)= =0AUGC-Dr. D. S. Kothari Post Doctoral Fellow=0ADepartment of Chemical Scie= nces=0ATezpur University=0ATezpur- ASSAM=0AINDIA=0A=0A=0A=0A-=3D This is au= tomatically added to each message by the mailing script =3D-=0ATo recover t= he email address of the author of the message, please change=0Athe strange = characters on the top line to the -.- sign. You can also=0Alook up the X-Orig= inal-From: line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY-.-c= cl.net or use:=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_messag= e=0A=0A=0A=A0 =A0= =A0=0A=0ASubscribe/Unsubsc= ribe: =0A=A0 =A0 =A0=0A=0ABefo= re posting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.ccl= .net/jobs =0AConferences: http://server.ccl.net/chemistry/announcements/con= ferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/inde= x.shtml=0A=0A=0A=A0 = =A0 =A0=0A=0ARTFI: http://www.ccl.net/chemi= stry/aboutccl/instructions/ --435439028-1490379958-1344011729=:78868 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Dr.= Kumar,

What that you fo= und barely is not a TS. It is a complex between reactant and product (if yo= u are studying a 2 component reaction). Many reactions in gas phase or in a= bsence of solvent molecules has no real barrier. For instance the well-know= n SN1 reaction in absence of solvent molecules has just one TS since the se= cond TS, which can be found in all text books, is due to solvent reorganiza= tion around Nu and carbocation.

I am not aware of th= e reaction that you are studying but this reaction might be of a similar cl= ass of reactions. Be careful about interpretation of reaction mechanism in = gas phase and absence of solvent molecules.

Best wishes,

Cina

=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Cina Foroutan-Nejad, Ph.D.

http://ind= ependent.academia.edu/CinaForoutanNejad

F= rom: Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com <= owner-chemistry-.-ccl.net>
To: "Foroutan-Nejad, Cina " <canyslopus-.-yahoo.co.uk> Sent: Friday, 3 August = 2012, 17:35
Subject: C= CL: Negative Barrier Height

Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__r= ediffmail.com]
Dear All,
I am doing some calculation on reaction mech= anism. I have optimized transition states. But the problem is that it is ch= aracterized by low vibrational frequency (<100 cm-1). The calculated bar= rier heights are negative. Whether it is possible? May negative barrier hei= ghts for TS are acceptable for understanding of any reaction mechanism?
= Any suggestions is highly appreciated.

Sincerely
Bhupesh K= umar Mishra(Ph.D.)
UGC-Dr. D. S. Kothari Post Doctoral Fellow
Departm= ent of Chemical Sciences
Tezpur University
Tezpur- ASSAM
INDIA
=

-=3D This is automatically added to each message by the mailing= script =3D-
To recover the email address of the author of the message, = please change
the strange characters on the top line to the -.- sign. You = can also
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--435439028-1490379958-1344011729=:78868-- From owner-chemistry@ccl.net Fri Aug 3 14:41:00 2012 From: "George Fitzgerald George.Fitzgerald,,accelrys.com" To: CCL Subject: CCL: Negative Barrier Height Message-Id: <-47316-120803140329-17052-zbt0gDvjpDKE5NIRfk+6cQ+/-server.ccl.net> X-Original-From: George Fitzgerald Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 3 Aug 2012 11:03:17 -0700 MIME-Version: 1.0 Sent to CCL by: George Fitzgerald [George.Fitzgerald*o*accelrys.com] Following up on Luke's suggestion about complexes, a method like IRC will find those. Also consider whether your computational method is accurate enough. Presumably you are doing this with electronic structure methods, probably DFT? Some functionals simply get the barrier wrong. GGA, for example, often get barriers of H migration too low. -george fitzgerald -----Original Message----- > From: owner-chemistry+gfitzgerald==accelrys.com-$-ccl.net [mailto:owner-chemistry+gfitzgerald==accelrys.com-$-ccl.net] On Behalf Of Dr. Bhupesh Kumar Mishra bhupesh_chem(_)rediffmail.com Sent: Friday, August 03, 2012 7:06 AM To: George Fitzgerald Subject: CCL: Negative Barrier Height Sent to CCL by: "Dr. Bhupesh Kumar Mishra" [bhupesh_chem__rediffmail.com] Dear All, I am doing some calculation on reaction mechanism. I have optimized transition states. But the problem is that it is characterized by low vibrational frequency (<100 cm-1). The calculated barrier heights are negative. Whether it is possible? May negative barrier heights for TS are acceptable for understanding of any reaction mechanism? Any suggestions is highly appreciated. Sincerely Bhupesh Kumar Mishra(Ph.D.) UGC-Dr. D. S. Kothari Post Doctoral Fellow Department of Chemical Sciences Tezpur University Tezpur- ASSAM INDIAhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt