From owner-chemistry@ccl.net Sun Jun 16 11:12:01 2013 From: "Errol Lewars elewars__trentu.ca" To: CCL Subject: CCL:G: TS optimization help! Message-Id: <-48830-130616111012-2871-FwP/soB0O1X1jLrZz765Yg ~ server.ccl.net> X-Original-From: Errol Lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 16 Jun 2013 11:10:21 -0400 MIME-Version: 1.0 Sent to CCL by: Errol Lewars [elewars:-:trentu.ca] 2013 June 16 "In order to obtain the TS structure, I first tried QST2 using optimized reactant and product structure. Didn't work out". QST2 is said to work better if instead of using as input the *optimized* reactant and product you distort each toward the other, i.e toward the transition state. You might also try taking one of the two minima and doing a scan, altering a geometric parameter in the TS direction; then submitting the highest point on the IRC-like curve (assuming you get such a curve) to a TS optimization/freq. E. Lewars == Joseph Takayama sjtakayama(~)gmail.com wrote: > Sent to CCL by: "Joseph Takayama" [sjtakayama*gmail.com] > Hi Everyone, > > I'm trying to reproduce the TS structure optimization which is already > reported in the paper. > > First, I prepared the structures of the reactant and the product from the > scratch and optimized them using the same basis functions as reported. > Obtained optimized structures seems similar to those reported and energy > difference between reactant and product also matched to the value in the > paper. > > In order to obtain the TS structure, I first tried QST2 using optimized > reactant and product structure. Didn't work out. > > Some key bond lengths of the TS structure are also reported in the paper. > So next, I freezed 2 key bond lengths using modredundant option and optimized > the rest. > Obtained structure seems quite similar to the TS structure in the paper. > >> From that structure, I tried Opt=(ts, calcfc, noeigentest), with or without > "tight" option and Opt=(QST3, calcfc). > However, every time I tried, optimization goes to the structure far away from > the TS structure that I want. > > Is there any tips to lead the optimization to the TS structure that I want? > Or is there any options that prevents structure to go too far away from the > initial structure? > I'm using Gaussian 09. > > Any comment would be appreciated! > > Joseph Takayama > sjtakayama_-_gmail.com> > From owner-chemistry@ccl.net Sun Jun 16 15:48:01 2013 From: "S. T. sjtakayama(~)gmail.com" To: CCL Subject: CCL: TS optimization help! Message-Id: <-48831-130616145434-11146-6ty23C/ez9ysQ4yY9zRPgw#server.ccl.net> X-Original-From: "S. T." Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response Date: Mon, 17 Jun 2013 03:54:41 +0900 MIME-Version: 1.0 Sent to CCL by: "S. T." [sjtakayama~~gmail.com] Thank you very much for your comment! > QST2 is said to work better if instead of using as input the *optimized* > reactant and product you distort each toward the other, i.e toward the > transition state. I'll definetelly try qst2 again using 2 structures closer to TS. > You might also try taking one of the two minima and doing a scan, altering > a geometric parameter in the TS direction; then submitting the highest > point on the IRC-like curve (assuming you get such a curve) to a TS > optimization/freq. Yes, in the original paper, authers obtained the initial TS structure using scan. The bond length they used for scan in TS structure is repoted in the paper so I used that bond length to get my initial TS structure. Maybe I should do the whole scan too and use 2 structure around TS to do qst2. Joseph From owner-chemistry@ccl.net Sun Jun 16 17:46:00 2013 From: "Adel El-Azhary azhary*ksu.edu.sa" To: CCL Subject: CCL: Hydrogen bond of sulfur containing molecules Message-Id: <-48832-130616063850-21706-8C0g+ljStKNIOw0DC7utbA]=[server.ccl.net> X-Original-From: "Adel El-Azhary" Date: Sun, 16 Jun 2013 06:38:47 -0400 Sent to CCL by: "Adel El-Azhary" [azhary^ksu.edu.sa] Dear all, Does anyone know a study of the estimate of the hydrogen bond in sulfur containing molecules? I made an intensive search but could not get any solid conclusion. Best regards, Adel El-Azhary Chemistry Department, Faculty of Science King Saud University P.O. Box 2455 Riyadh, 11451 Saudi Arabia From owner-chemistry@ccl.net Sun Jun 16 22:16:00 2013 From: "Mehboob Alam mehboob.cu]-[gmail.com" To: CCL Subject: CCL:G: TS optimization help! Message-Id: <-48833-130616044404-15557-iCh23T2jCJZLPEKQbLPv/g..server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=047d7bd6b9001f7b3304df417bf3 Date: Sun, 16 Jun 2013 14:13:58 +0530 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu%a%gmail.com] --047d7bd6b9001f7b3304df417bf3 Content-Type: text/plain; charset=ISO-8859-1 Hi Joseph, Although I'm not an expert for TS optimization but whenever I try to optimize the TS I use to do it using QST3 method and it always produces the correct TS structure. So, I think you must try to optimize TS using QST3 directly on the guess geometry. I mean optimize the reactant and product. Then make an appropriate guess for TS and finally use the three structures (for QST3 method) and let the program to find the TS. Hope it will help. Regards, Mehboob On Sun, Jun 16, 2013 at 7:56 AM, Joseph Takayama sjtakayama(~)gmail.com < owner-chemistry]*[ccl.net> wrote: > > Sent to CCL by: "Joseph Takayama" [sjtakayama*gmail.com] > Hi Everyone, > > I'm trying to reproduce the TS structure optimization which is already > reported in the paper. > > First, I prepared the structures of the reactant and the product from the > scratch and optimized them using the same basis functions as reported. > Obtained optimized structures seems similar to those reported and energy > difference between reactant and product also matched to the value in the > paper. > > In order to obtain the TS structure, I first tried QST2 using optimized > reactant and product structure. Didn't work out. > > Some key bond lengths of the TS structure are also reported in the paper. > So next, I freezed 2 key bond lengths using modredundant option and > optimized > the rest. > Obtained structure seems quite similar to the TS structure in the paper. > > > From that structure, I tried Opt=(ts, calcfc, noeigentest), with or > without > "tight" option and Opt=(QST3, calcfc). > However, every time I tried, optimization goes to the structure far away > from > the TS structure that I want. > > Is there any tips to lead the optimization to the TS structure that I want? > Or is there any options that prevents structure to go too far away from the > initial structure? > I'm using Gaussian 09. > > Any comment would be appreciated! > > Joseph Takayama > sjtakayama_-_gmail.com> > > --047d7bd6b9001f7b3304df417bf3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Joseph,

Although I'm not an expert for TS optimiz= ation but whenever I try to optimize the TS I use to do it using QST3 metho= d and it always produces the correct TS structure. So, I think you must try= to optimize TS using QST3 directly on the guess geometry.=A0
I mean optimize the reactant and product. Then make an appropriate gue= ss for TS and finally use the three structures (for QST3 method) and let th= e program to find the TS.

Hope it will help.

Regards,
Mehboob

On Sun, Jun 16, 2013 at 7:56 AM, Joseph Takayama sjtakayama(~)gmail.com <owner-chemistry]*[ccl.net>= wrote:

Sent to CCL by: "Joseph =A0Takayama" [sjtakayama*gmail.com]
Hi Everyone,

I'm trying to reproduce the TS structure optimization which is already<= br> reported in the paper.

First, I prepared the structures of the reactant and the product from the scratch and optimized them using the same basis functions as reported.
Obtained optimized structures seems similar to those reported and energy difference between reactant and product also matched to the value in the paper.

In order to obtain the TS structure, I first tried QST2 using optimized
reactant and product structure. Didn't work out.

Some key bond lengths of the TS structure are also reported in the paper. So next, I freezed 2 key bond lengths using modredundant option and optimiz= ed
the rest.
Obtained structure seems quite similar to the TS structure in the paper.
> From that structure, I tried Opt=3D(ts, calcfc, noeigentest), with or = without
"tight" option and Opt=3D(QST3, calcfc).
However, every time I tried, optimization goes to the structure far away fr= om
the TS structure that I want.

Is there any tips to lead the optimization to the TS structure that I want?=
Or is there any options that prevents structure to go too far away from the=
initial structure?
I'm using Gaussian 09.

Any comment would be appreciated!

Joseph Takayama
sjtakayama_-_gm= ail.com



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