Dear Panesun Tukur , While I agree with Corentin Lefebvre in his procedure for reactions whose transition state structure you don't know or cannot anticipate, I don't think it is well suited here. For the particular case of a nucleophilic substitution like yours, in which the archetypal structure of the transition state is very well known (planarization of the affected carbon center, incoming and leaving groups in a ~180º angle), I think the fastest approach will be to directly draw a structure that resembles the transition state, and start the optimization. Just draw a pentacoordinated, trigonal bipyramid C, and replace the hydrogens in a linear arrangement by the chloride and the acetate, then make the C-O and C-Cl distances of around 2 A, and optimize as TS. Then, of course, run the standard tests (frequencies and IRC) Hope you find it helpful
Dear Panesun Tukur , While I agree with Corentin Lefebvre in his procedure for reactions whose transition state structure you don't know or cannot anticipate, I don't think it is well suited here. For the particular case of a nucleophilic substitution like yours, in which the archetypal structure of the transition state is very well known (planarization of the affected carbon center, incoming and leaving groups in a ~180º angle), I think the fastest approach will be to directly draw a structure that resembles the transition state, and start the optimization. Just draw a pentacoordinated, trigonal bipyramid C, and replace the hydrogens in a linear arrangement by the chloride and the acetate, then make the C-O and C-Cl distances of around 2 A, and optimize as TS. Then, of course, run the standard tests (frequencies and IRC) Hope you find it helpful
Dear Enrique Manuel Arpa, I just wish to verify if I properly understood what you mean. is the figure below the initial input structure based on your explanation? or the oxygen is the O11 should be directly bonded to C1?
Dear Enrique Manuel Arpa, I just wish to verify if I properly understood what you mean. is the figure below the initial input structure based on your explanation? or the oxygen is the O11 should be directly bonded to C1?
1. I'm used to start from the products and perform a conformational research when needed (with the help of CREST from XTB, totally free). 2. Instead of using QST method implemented in Gaussian, I perform a scan at lower level of theory with the atomic coordinates from the geometry of my product I obtained using "OPT=ADDREDUNDANT" (MODREDUNDANT is also working) following at the end of atom coordinates and an empty line by this indication: B ATOMIC_NUMBER_1 ATOMIC_NUMBER_2 S NUMBER_OF_STEPS STEPS As an example, a scan between atom 1 and atom 2 pulling away with 30 steps of 0.1 a.u.: B 1 2 S 30 0.1 The scan is performed with optimization at each step if you ask with "OPT" at the beginning of your input file. Others instruction could be provided such as a double scan for concerted mechanism {If you put a negative number of steps, you will decrease the distance between the two considered atoms). 3. I analyse with Molden (free) the point for which the maximum in energy is reached and output coordinates for this geometry. This is my guess for my TS research. 4. I usually use these instructions for my TS optimization: "OPT=(TS, CALCALL, NOEIGENTEST)" with of course a the keyword "FREQ" to be sure I reach a saddle point. 5. When everything's fine (one negative force constant, so one imaginary frequency) I perform two IRC calculations (reverse and forward) with those keywords for example: "irc=(calcall,forward,maxcycle=100, maxpoints=30,stepsize=10)". Calcall makes the calculation to be longer, but it generally avoids error termination. Maxpoints and stepsize can of course, be changed, depending on your system. 5.bis. When there are problems with IRC calculation, I sometimes move a bit the geometry towards the reactant and the product to be a very little bit far from the TS geometry towards the reactant and the product and perform a optimization with "OPT=STEEP", that allows me to have my reaction path. 6. From the last geometry obtained from IRC_reverse, I perform an optimization calculation of my reactant. 7. I finish with an optimisation of my reactant and product as well as my TS at a better level of theory, with solvent (if needed) and "INT=ULTRAFINE" (it may be the default in Gaussian 16 but not sure in Gaussian 09) if you work with DFT. 8. For analysis of your reaction, you could consider KistHelp program (free) that will surely be helpful.
1. I'm used to start from the products and perform a conformational research when needed (with the help of CREST from XTB, totally free). 2. Instead of using QST method implemented in Gaussian, I perform a scan at lower level of theory with the atomic coordinates from the geometry of my product I obtained using "OPT=ADDREDUNDANT" (MODREDUNDANT is also working) following at the end of atom coordinates and an empty line by this indication: B ATOMIC_NUMBER_1 ATOMIC_NUMBER_2 S NUMBER_OF_STEPS STEPS As an example, a scan between atom 1 and atom 2 pulling away with 30 steps of 0.1 a.u.: B 1 2 S 30 0.1 The scan is performed with optimization at each step if you ask with "OPT" at the beginning of your input file. Others instruction could be provided such as a double scan for concerted mechanism {If you put a negative number of steps, you will decrease the distance between the two considered atoms). 3. I analyse with Molden (free) the point for which the maximum in energy is reached and output coordinates for this geometry. This is my guess for my TS research. 4. I usually use these instructions for my TS optimization: "OPT=(TS, CALCALL, NOEIGENTEST)" with of course a the keyword "FREQ" to be sure I reach a saddle point. 5. When everything's fine (one negative force constant, so one imaginary frequency) I perform two IRC calculations (reverse and forward) with those keywords for example: "irc=(calcall,forward,maxcycle=100, maxpoints=30,stepsize=10)". Calcall makes the calculation to be longer, but it generally avoids error termination. Maxpoints and stepsize can of course, be changed, depending on your system. 5.bis. When there are problems with IRC calculation, I sometimes move a bit the geometry towards the reactant and the product to be a very little bit far from the TS geometry towards the reactant and the product and perform a optimization with "OPT=STEEP", that allows me to have my reaction path. 6. From the last geometry obtained from IRC_reverse, I perform an optimization calculation of my reactant. 7. I finish with an optimisation of my reactant and product as well as my TS at a better level of theory, with solvent (if needed) and "INT=ULTRAFINE" (it may be the default in Gaussian 16 but not sure in Gaussian 09) if you work with DFT. 8. For analysis of your reaction, you could consider KistHelp program (free) that will surely be helpful.
Dear Panesun Tukur ,
While I agree with Corentin Lefebvre in his procedure for reactions whose transition state structure you don't know or cannot anticipate, I don't think it is well suited here. For the particular case of a nucleophilic substitution like yours, in which the archetypal structure of the transition state is very well known (planarization of the affected carbon center, incoming and leaving groups in a ~180º angle), I think the fastest approach will be to directly draw a structure that resembles the transition state, and start the optimization. Just draw a pentacoordinated, trigonal bipyramid C, and replace the hydrogens in a linear arrangement by the chloride and the acetate, then make the C-O and C-Cl distances of around 2 A, and optimize as TS. Then, of course, run the standard tests (frequencies and IRC)
Hope you find it helpful
Dear Panesun Tukur ,
While I agree with Corentin Lefebvre in his procedure for reactions whose transition state structure you don't know or cannot anticipate, I don't think it is well suited here. For the particular case of a nucleophilic substitution like yours, in which the archetypal structure of the transition state is very well known (planarization of the affected carbon center, incoming and leaving groups in a ~180º angle), I think the fastest approach will be to directly draw a structure that resembles the transition state, and start the optimization. Just draw a pentacoordinated, trigonal bipyramid C, and replace the hydrogens in a linear arrangement by the chloride and the acetate, then make the C-O and C-Cl distances of around 2 A, and optimize as TS. Then, of course, run the standard tests (frequencies and IRC)
Hope you find it helpful
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Dear Enrique Manuel Arpa, I just wish to verify if I properly understood what you mean. is the figure below the initial input structure based on your explanation? or the oxygen is the O11 should be directly bonded to C1?
Dear Enrique Manuel Arpa, I just wish to verify if I properly understood what you mean. is the figure below the initial input structure based on your explanation? or the oxygen is the O11 should be directly bonded to C1?
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Dear Panesun Tukur ,
I allow myself to copy paste an answer I made some weeks ago on a method I'm used to find a transition state:
https://www.researchgate.net/post/Could_you_please_give_the_programme_for_finding_transition_state_for_a_reaction_using_gaussian_09
1. I'm used to start from the products and perform a conformational research when needed (with the help of CREST from XTB, totally free).
2. Instead of using QST method implemented in Gaussian, I perform a scan at lower level of theory with the atomic coordinates from the geometry of my product I obtained using "OPT=ADDREDUNDANT" (MODREDUNDANT is also working) following at the end of atom coordinates and an empty line by this indication:
B ATOMIC_NUMBER_1 ATOMIC_NUMBER_2 S NUMBER_OF_STEPS STEPS
As an example, a scan between atom 1 and atom 2 pulling away with 30 steps of 0.1 a.u.:
B 1 2 S 30 0.1
The scan is performed with optimization at each step if you ask with "OPT" at the beginning of your input file. Others instruction could be provided such as a double scan for concerted mechanism {If you put a negative number of steps, you will decrease the distance between the two considered atoms).
3. I analyse with Molden (free) the point for which the maximum in energy is reached and output coordinates for this geometry. This is my guess for my TS research.
4. I usually use these instructions for my TS optimization: "OPT=(TS, CALCALL, NOEIGENTEST)" with of course a the keyword "FREQ" to be sure I reach a saddle point.
5. When everything's fine (one negative force constant, so one imaginary frequency) I perform two IRC calculations (reverse and forward) with those keywords for example: "irc=(calcall,forward,maxcycle=100,
maxpoints=30,stepsize=10)". Calcall makes the calculation to be longer, but it generally avoids error termination. Maxpoints and stepsize can of course, be changed, depending on your system.
5.bis. When there are problems with IRC calculation, I sometimes move a bit the geometry towards the reactant and the product to be a very little bit far from the TS geometry towards the reactant and the product and perform a optimization with "OPT=STEEP", that allows me to have my reaction path.
6. From the last geometry obtained from IRC_reverse, I perform an optimization calculation of my reactant.
7. I finish with an optimisation of my reactant and product as well as my TS at a better level of theory, with solvent (if needed) and "INT=ULTRAFINE" (it may be the default in Gaussian 16 but not sure in Gaussian 09) if you work with DFT.
8. For analysis of your reaction, you could consider KistHelp program (free) that will surely be helpful.
Dear Panesun Tukur ,
I allow myself to copy paste an answer I made some weeks ago on a method I'm used to find a transition state:
https://www.researchgate.net/post/Could_you_please_give_the_programme_for_finding_transition_state_for_a_reaction_using_gaussian_09
1. I'm used to start from the products and perform a conformational research when needed (with the help of CREST from XTB, totally free).
2. Instead of using QST method implemented in Gaussian, I perform a scan at lower level of theory with the atomic coordinates from the geometry of my product I obtained using "OPT=ADDREDUNDANT" (MODREDUNDANT is also working) following at the end of atom coordinates and an empty line by this indication:
B ATOMIC_NUMBER_1 ATOMIC_NUMBER_2 S NUMBER_OF_STEPS STEPS
As an example, a scan between atom 1 and atom 2 pulling away with 30 steps of 0.1 a.u.:
B 1 2 S 30 0.1
The scan is performed with optimization at each step if you ask with "OPT" at the beginning of your input file. Others instruction could be provided such as a double scan for concerted mechanism {If you put a negative number of steps, you will decrease the distance between the two considered atoms).
3. I analyse with Molden (free) the point for which the maximum in energy is reached and output coordinates for this geometry. This is my guess for my TS research.
4. I usually use these instructions for my TS optimization: "OPT=(TS, CALCALL, NOEIGENTEST)" with of course a the keyword "FREQ" to be sure I reach a saddle point.
5. When everything's fine (one negative force constant, so one imaginary frequency) I perform two IRC calculations (reverse and forward) with those keywords for example: "irc=(calcall,forward,maxcycle=100,
maxpoints=30,stepsize=10)". Calcall makes the calculation to be longer, but it generally avoids error termination. Maxpoints and stepsize can of course, be changed, depending on your system.
5.bis. When there are problems with IRC calculation, I sometimes move a bit the geometry towards the reactant and the product to be a very little bit far from the TS geometry towards the reactant and the product and perform a optimization with "OPT=STEEP", that allows me to have my reaction path.
6. From the last geometry obtained from IRC_reverse, I perform an optimization calculation of my reactant.
7. I finish with an optimisation of my reactant and product as well as my TS at a better level of theory, with solvent (if needed) and "INT=ULTRAFINE" (it may be the default in Gaussian 16 but not sure in Gaussian 09) if you work with DFT.
8. For analysis of your reaction, you could consider KistHelp program (free) that will surely be helpful.
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Enrique Manuel Arpa
Thank you for your clear insights. I'm grateful
Enrique Manuel Arpa
Thank you for your clear insights. I'm grateful
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Panesun Tukur ,
Is the O11 the one should be attached to C1, it is the atom that "attacks" the electrophilic C1. See image attached.
Panesun Tukur ,
Is the O11 the one should be attached to C1, it is the atom that "attacks" the electrophilic C1. See image attached.
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Thank you both for the awesome contributions.I really appreciate.
Thank you both for the awesome contributions.I really appreciate.
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