From owner-chemistry@ccl.net Thu Jan 2 00:29:00 2014 From: "Joseph Takayama sjtakayama^gmail.com" To: CCL Subject: CCL:G: Did I find proper TS or...? Message-Id: <-49498-140102002802-15424-HYdNtXetJS2ps197Pd3RZA]^[server.ccl.net> X-Original-From: "Joseph Takayama" Date: Thu, 2 Jan 2014 00:28:00 -0500 Sent to CCL by: "Joseph Takayama" [sjtakayama-*-gmail.com] Dear CCL subscribers, I ran transition state structure optimization of one molecule using Gaussian09. The optimization didn't finish even after 45 optimization steps, so I picked one structure which has the lowest RMS gradient norm and ran freq calculation. As a result, I found that the structure I picked actuary has only one negative frequency mode which properly connect reactant and product structures. In this case, is it ok to assume that I found the right TS structure although initial optimization calculation didn't finish as usual? Thank you in advance for your comments. Joseph From owner-chemistry@ccl.net Thu Jan 2 01:04:00 2014 From: "swastikab-x-jncasr.ac.in" To: CCL Subject: CCL: MOMO-LUMO energy gap. Message-Id: <-49499-140101234501-28903-DhvkCYMZPYuc+pChcLNVDw++server.ccl.net> X-Original-From: swastikab..jncasr.ac.in Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8 Date: Thu, 2 Jan 2014 10:14:08 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: swastikab[a]jncasr.ac.in Dear sir, According to FMO theory bond is created by the HOMO(Nu)-LUMO(El) interaction, any influences on the reactants, or transition state geometry, that causes strong HOMO(Nu)-LUMO(El) interaction, stabilizes the transition state and makes the reaction faster. Hence large HOMO-LUMO gap in TS might talk about the stability of the transition state. On the other hand global reactivity descriptor hardness(which is nothing but the reflection of HOMO-LUMO energy difference) is to describe the intrinsic stability ans reactivity of the reactants and products. With regards, Swastika Swastika Banerjee Ph.D (SRF) New Chemistry Unit/Theoretical Sciences Unit JNCASR Bangalore-64 From owner-chemistry@ccl.net Thu Jan 2 02:56:00 2014 From: "Dr. Robin Haunschild H===unschild.de" To: CCL Subject: CCL:G: Did I find proper TS or...? Message-Id: <-49500-140102025238-29520-5vLIyqrmaUSHK3+A5OLqWA[A]server.ccl.net> X-Original-From: "Dr. Robin Haunschild" Content-Type: multipart/alternative; boundary="----C8D0PTTDI9EV1QVFSOC4KYY1D63EK6" Date: Thu, 02 Jan 2014 08:52:33 +0100 MIME-Version: 1.0 Sent to CCL by: "Dr. Robin Haunschild" [H : unschild.de] ------C8D0PTTDI9EV1QVFSOC4KYY1D63EK6 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Dear Joseph, You did not find the TS, unfortunately=2E The gradient vanish= es at every TS=2E You will have to continue the TS search until the gradien= t vanishes=2E If you didn't do so already, please try the QST3 option as a= n alternative=2E Best regards, Robin "Joseph Takayama sjtakayama^gmai= l=2Ecom" schrieb: > >Sent to CCL by: "Joseph T= akayama" [sjtakayama-*-gmail=2Ecom] >Dear CCL subscribers, > >I ran transit= ion state structure optimization of one molecule using >Gaussian09=2E >The = optimization didn't finish even after 45 optimization steps, so I >picked = >one structure which has the lowest RMS gradient norm and ran freq >calcula= tion=2E >As a result, I found that the structure I picked actuary has only = one >negative >frequency mode which properly connect reactant and product = structures=2E >In this case, is it ok to assume that I found the right TS s= tructure >although >initial optimization calculation didn't finish as usua= l? > >Thank you in advance for your comments=2E > >Joseph > > > >-=3D This = is automatically added to each message by the mailing script =3D- >To recov= er the email address of the author of the message, please >change >the stra= nge characters on the top line to the [-] sign=2E You can also >look up the X= -Original-From: line in the mail header=2E > >E-mail to subscribers: CHEMIS= TRY[-]ccl=2Enet or use: > http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_me= ssage > >E-mail to administrators: CHEMISTRY-REQUEST[-]ccl=2Enet or use > = http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message > >Subscribe/Unsubscr= ibe: > http://www=2Eccl=2Enet/chemistry/sub_unsub=2Eshtml > >Before p= osting, check wait time at: http://www=2Eccl=2Enet > >Job: http://www=2Eccl= =2Enet/jobs >Conferences: http://server=2Eccl=2Enet/chemistry/announcement= s/conferences/ > >Search Messages: http://www=2Eccl=2Enet/chemistry/searchc= cl/index=2Eshtml > >If your mail bounces from CCL with 5=2E7=2E1 error, che= ck: > http://www=2Eccl=2Enet/spammers=2Etxt > >RTFI: http://www=2Eccl= =2Enet/chemistry/aboutccl/instructions/ -- Sent from my Xperia Tablet Z ------C8D0PTTDI9EV1QVFSOC4KYY1D63EK6 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Joseph,

You did not find the TS, unf= ortunately=2E The gradient vanishes at every TS=2E You will have to continu= e the TS search until the gradient vanishes=2E

If you didn't d= o so already, please try the QST3 option as an alternative=2E


= Best regards,

Robin



&= quot;Joseph Takayama sjtakayama^gmail=2Ecom<= /a>" <owner-chemistry[-]ccl=2Enet> schrieb:

Sent to C=
CL by: "Joseph  Takayama" [sjtakayama-*-gmai=
l=2Ecom]
Dear CCL subscribers,

I ran transition state s=
tructure optimization of one molecule using Gaussian09=2E
The optimiza=
tion didn't finish even after 45 optimization steps, so I picked 
one =
structure which has the lowest RMS gradient norm and ran freq calculation=
=2E
As a result, I found that the structure I picked actuary has only =
one negative 
frequency mode which properly connect reactant and produ=
ct structures=2E
In this case, is it ok to assume that I found the rig=
ht TS structure although 
initial optimization calculation didn't fini=
sh as usual?

Thank you in advance for your comments=2E

Joseph



-=3D This is automatically added to each me=
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--
Sent from my Xperia Tablet Z ------C8D0PTTDI9EV1QVFSOC4KYY1D63EK6-- From owner-chemistry@ccl.net Thu Jan 2 12:40:10 2014 From: "Jan Halborg Jensen jhjensen]^[chem.ku.dk" To: CCL Subject: CCL: Computational Chemistry Highlights: December issue Message-Id: <-49502-140102055140-28737-yrhtZP1z/pBBSa4AE+cWiA .. server.ccl.net> X-Original-From: Jan Halborg Jensen Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_3960ACC4F7E1574EBB19AFC61B2389FD9F816D3FP1KITMBX03WC02u_" Date: Thu, 2 Jan 2014 10:51:21 +0000 MIME-Version: 1.0 Sent to CCL by: Jan Halborg Jensen [jhjensen_+_chem.ku.dk] --_000_3960ACC4F7E1574EBB19AFC61B2389FD9F816D3FP1KITMBX03WC02u_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable The December issue of Computational Chemistry Highlights is out. CCH is an overlay journal tha= t identifies the most important papers in computational and theoretical che= mistry published in the last 1-2 years. CCH is not affiliated with any publ= isher: it is a free resource run by scientists for scientists. You can read= more about it here. Table of content for this issue features contributions from CCH editor Stev= en Bachrach: Six Pyranoside Forms of Free 2-Deoxy-D-ribose Computation-aided structure determination Interested in more? There are many ways to subscribe to CCH updates. --_000_3960ACC4F7E1574EBB19AFC61B2389FD9F816D3FP1KITMBX03WC02u_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

The December issue of Computationa= l Chemistry Highlights is out.


CCH is an ove= rlay journal that identifies the most important papers in computat= ional and theoretical chemistry published in the last 1-2 years. CCH is not= affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here.


Table of content for this issue features contributions from CCH editor Stev= en Bachrach:


= --_000_3960ACC4F7E1574EBB19AFC61B2389FD9F816D3FP1KITMBX03WC02u_-- From owner-chemistry@ccl.net Thu Jan 2 14:04:00 2014 From: "Partha Sengupta anapspsmo(!)gmail.com" To: CCL Subject: CCL: MOMO-LUMO energy gap. Message-Id: <-49503-140102135630-8119-MER7+ERLzZINH5Lwsbh+gA%%server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=047d7b6dd09c9f4e0a04eefee85f Date: Thu, 2 Jan 2014 21:31:38 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo-$-gmail.com] --047d7b6dd09c9f4e0a04eefee85f Content-Type: text/plain; charset=ISO-8859-1 Raman, Please send me the paper, I have no accessibility of that paper. On Thu, Jan 2, 2014 at 10:14 AM, swastikab-x-jncasr.ac.in < owner-chemistry- -ccl.net> wrote: > > Sent to CCL by: swastikab[a]jncasr.ac.in > Dear sir, > > According to FMO theory bond is created by the HOMO(Nu)-LUMO(El) > interaction, any influences on the reactants, or transition state geometry, > that causes strong HOMO(Nu)-LUMO(El) interaction, stabilizes the transition > state and makes the reaction faster. Hence large HOMO-LUMO gap in TS might > talk about the stability of the transition state. > On the other hand global reactivity descriptor hardness(which is nothing > but the reflection of HOMO-LUMO energy difference) is to describe the > intrinsic stability ans reactivity of the reactants and products. > > With regards, > Swastika > > Swastika Banerjee > Ph.D (SRF) > New Chemistry Unit/Theoretical Sciences Unit > JNCASR > Bangalore-64> > > -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --047d7b6dd09c9f4e0a04eefee85f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
=A0
Raman,
Please send me the paper, I have no acce= ssibility of that paper.


On Thu, Jan 2, 2014 at 10:14 AM, swastikab-x-jncasr.ac.in <<= a href=3D"mailto:owner-chemistry- -ccl.net" target=3D"_blank">owner-chemistry= - -ccl.net> wrote:

Sent to CCL by: swastikab[a]jncasr.ac.in
Dear sir,

According to FMO theory bond is created by the HOMO(Nu)-LUMO(El) interactio= n, any influences on the reactants, or transition state geometry, that caus= es strong HOMO(Nu)-LUMO(El) interaction, stabilizes the transition state an= d makes the reaction faster. Hence large HOMO-LUMO gap in TS might talk abo= ut the stability of the transition state.
On the other hand global reactivity descriptor hardness(which is nothing bu= t the reflection of HOMO-LUMO energy difference) is to describe the intrins= ic stability ans reactivity of the reactants and products.

With regards,
Swastika

Swastika Banerjee
Ph.D (SRF)
New Chemistry Unit/Theoretical Sciences Unit
JNCASR
Bangalore-64



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Dr. Partha Sarathi Seng= upta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan
--047d7b6dd09c9f4e0a04eefee85f-- From owner-chemistry@ccl.net Thu Jan 2 17:32:00 2014 From: "Mark Zottola mzottola+/-gmail.com" To: CCL Subject: CCL:G: Did I find proper TS or...? Message-Id: <-49504-140102173103-9513-y/234wkLA4kSMU7TI7XwAA=-=server.ccl.net> X-Original-From: Mark Zottola Content-Type: multipart/alternative; boundary=047d7bb04c00d564e104ef045813 Date: Thu, 2 Jan 2014 17:30:56 -0500 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola|,|gmail.com] --047d7bb04c00d564e104ef045813 Content-Type: text/plain; charset=ISO-8859-1 Since the structure after 45 steps has only one imaginary frequency, you can restart the optimization from the frequency job you ran. Opt=ts,readfc would work. If you do not have any large rotational imaginary frequencies, then this should work. If you have a smallish system with, IIRC, a z-matrix containing less then 50 variables, you can use opt=ts,ef,calcfc. You must add a 10 (again IIRC) after the first variable value to indicate tha is the mode to follow to find a ts. Of course, if you have optimized reactant and product structures with the same numbering as your TS structure, you can do qst3 as was mentioned earlier. Finding TS structures is an art. There are manifold ways to find them and you will find the optimal ways which work on the systems you are interested in... Don't be afraid to make a mistake or two or seven! Good Luck On Thu, Jan 2, 2014 at 12:28 AM, Joseph Takayama sjtakayama^gmail.com < owner-chemistry#,#ccl.net> wrote: > > Sent to CCL by: "Joseph Takayama" [sjtakayama-*-gmail.com] > Dear CCL subscribers, > > I ran transition state structure optimization of one molecule using > Gaussian09. > The optimization didn't finish even after 45 optimization steps, so I > picked > one structure which has the lowest RMS gradient norm and ran freq > calculation. > As a result, I found that the structure I picked actuary has only one > negative > frequency mode which properly connect reactant and product structures. > In this case, is it ok to assume that I found the right TS structure > although > initial optimization calculation didn't finish as usual? > > Thank you in advance for your comments. > > Joseph> > > --047d7bb04c00d564e104ef045813 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Since the structure after 45 steps has only one imaginary = frequency, you can restart the optimization from the frequency job you ran.= Opt=3Dts,readfc would work. =A0If you do not have any large rotational ima= ginary frequencies, then this should work.

If you have a smallish system with, IIRC, a z-matrix contain= ing less then 50 variables, you can use opt=3Dts,ef,calcfc. =A0You must add= a 10 (again IIRC) after the first variable value to indicate tha is the mo= de to follow to find a ts. =A0Of course, if you have optimized reactant and= product structures with the same numbering as your TS structure, you can d= o qst3 as was mentioned earlier.

Finding TS structures is an art. =A0There are manifold = ways to find them and you will find the optimal ways which work on the syst= ems you are interested in... Don't be afraid to make a mistake or =A0tw= o or seven!

Good Luck



On Thu, Jan 2, 2014 at 12:28 AM,= Joseph Takayama sjtakayama^gmail.com <owner-chemistry#,#ccl.net> wrote:

Sent to CCL by: "Joseph =A0Takayama" [sjtakayama-*-gmail.com]
Dear CCL subscribers,

I ran transition state structure optimization of one molecule using Gaussia= n09.
The optimization didn't finish even after 45 optimization steps, so I p= icked
one structure which has the lowest RMS gradient norm and ran freq calculati= on.
As a result, I found that the structure I picked actuary has only one negat= ive
frequency mode which properly connect reactant and product structures.
In this case, is it ok to assume that I found the right TS structure althou= gh
initial optimization calculation didn't finish as usual?

Thank you in advance for your comments.

Joseph



-=3D This is automatically added to each message by the mailing script =3D-=
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--047d7bb04c00d564e104ef045813-- From owner-chemistry@ccl.net Thu Jan 2 21:12:00 2014 From: "sjtakayama#,#gmail.com sjtakayama#,#gmail.com" To: CCL Subject: CCL: Did I find proper TS or...? Message-Id: <-49505-140102210701-6435-0imtK0aZiFMDCmXYUEed4g]~[server.ccl.net> X-Original-From: "sjtakayama*gmail.com" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 02 Jan 2014 18:06:48 -0800 MIME-Version: 1.0 Sent to CCL by: "sjtakayama/./gmail.com" [sjtakayama/./gmail.com] Thank you everyone for help! I'll try further to find right TS structure. Joseph