Transition State Search (QST2 & QST3) and IRC with Gaussian09

Theoretical evaluation of a reaction mechanism is all about finding the right transition states (TS) but there are no guarantees within the available methods to actually find the one we need. Chemical intuition in the proposal of a mechanism is paramount. Let’s remember that a TS is a critical point on a Potential Energy Surface (PES) that is a minimum in every dimension but one. For a PES with more than two degrees of freedom, a hyper-surface, envisioning the location of a TS is a bit tricky, in the case of a three dimensional PES (two degrees of freedom) the saddle point constitutes the location of the TS as depicted in figure 1 by a section of a revolution hyperboloid.


Fig1. Saddle point on a surface (min in one direction; max in the other)

Fig 1a Pringles chips -Yuck-. They exhibit a maximum on the direction parallel to the screen and a minimum on the direction perpendicular to the screen at the same point.

Fig 1a Pringles chips -Yuck-. They exhibit a maximum on the direction parallel to the screen and a minimum on the direction perpendicular to the screen at the same point.

The following procedure considers gas phase calculations. Nevertheless, the use of the SCRF keyword activates the implicit solvent calculation of choice in order to evaluate to some degree the solvent influence on the reaction energetics at different temperatures with the use of the temperature keyword.

The first step consists of a high level optimization of all minimums involved, such as reagents, products and intermediates, with a subsequent frequency analysis that includes no imaginary eigenvalues.

In order to find the structures of the transition states we use in Gaussian the Synchronous Transit-guided Quasi-Newton method [1] through the keywords QST2 or QST3. In the former case, coordinates for the reagents and products are needed as input; for the latter keyword, coordinates for the TS structure guess is needed also.



#p opt=(qst2,redundant) m062x/6-31++G(d,p) freq=noraman Temperature=373.15 SCRF=(Solvent=Water)

Title card for reagents

Cartesian Coordinates for reagents
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Title card for products

Cartesian Coordinates for products
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#p opt=(qst3,redundant) m062x/6-31++G(d,p) freq=noraman Temperature=373.15 SCRF=(Solvent=Water)

Title Card for reagents

Cartesian Coordinates for reagents
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Title card for products

Cartesian Coordinates for products
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Title card for TS
Cartesian Coordinates for TS
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NOTE: It is fundamental that the numbering order is kept constant throughout the molecular specifications of all two, or three, input structures. Hence, I recommend to build a set of molecules, save their structure, and then modified the coordinates on the same file to produce the following structure, that way the number for every atom will remain the same for every step.

As I wrote above, there are no guarantees of finding the right TS so many attempts are probably needed. Once we have the optimized structures for all the species involved in our mechanistic proposal we can plot their energies very simply with MS Excel the way we’ve previously described in this blog (reblogged from

Once we’ve succeeded in finding the structure of our TS we may run an Internal Reaction Coordinate (IRC) calculation. This calculation will connect the TS structure to those of the products and the reagents. Initial constant forces are required and these are commonly retrieved from the TS calculation checkpoint file through the RCFC keyword.


#p m062x/6-31++G(d,p) IRC=(Maxpoints=50,RCFC,phase=(2,1))Temperature=373.15 SCRF=(Solvent=Water) geom=allcheck

Title Card

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Finally, the IRC path can be visualized with GaussView from the Results menu. A successful IRC will link both structures along a single reaction coordinate proving that both reagents and products are linked by the obtained TS.

Hat tip to Howard Diaz who has become quite skillful in calculating these mechanisms as proven by his recent poster at the XII RMFQT a couple of weeks back. And as usual thanks to everyone who reads, comments, likes, recommends, rates and shares my silly little posts.

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About joaquinbarroso

Theoretical chemist in his early thirties, in love with life and deeply in love with his woman. I love science, baseball, literature, movies (perhaps even in that order). I'm passionate about food and lately wines have become a major hobby. In a nutshell I'm filled with regrets but also with hope, and that is called "living".

Posted on November 27, 2013, in Computational Chemistry, Gaussian, Models, Research, Theoretical Chemistry, White papers and tagged , , , , , , , , , , , . Bookmark the permalink. 10 Comments.

  1. Anya Skitnevskaya

    It’s a little misprint. In QST3 input you put: opt=(qst2…
    Nevertheless. Already for a long time I wanted to say thank you for your blog, you do a great and important work! :)

  2. I am trying to get a transition state having a complex molecular system with 4 H-bond. the The groups invoved for interaction are C=O and NH2. The distance between them is 4.5 angstrom initially. I got a transition state from it with 48 kCalmol(-). It seems that I have missed a transition state in between. What procedure should I take to get the transition state in between the H bonded initial complex and the proton shuttling TS?

  3. Thanks in support of sharing such a pleasant idea, paragraph is
    good, thats why i have read it fully

  4. Hola, estoy intentado proponer un estado de transición que es básicamente una disociación para el (CH3)3CC(O)OO—-NO2 pero cuando obtengo el TS la frecuencia negativa que encuentro es muy pequeña así que necesito mejorar esa frecuencia. Los keywords que estoy usando son
    # opt=(calcfc,tight,ts,noeigentest) freq ub3lyp/6-31++g(d,p)
    Me podría dar algunas recomendaciones que me ayuden a mejorar el cálculo?
    Muchas gracias.

    • Hola Diana!

      A que te refieres con muy pequeña? Ni en valor ni en intensidad (IR o RAMAN) necesitas que sea “grande” si corresponde al estado vibaracional que conecte tus reactivos con tus productos.
      Por lo que veo tu nivel de teoría es adecuado, si bien el uso de b3lyp pudiera acaso ser cuestionable aunque nosotros hemos obtenidos buenos resultados (reproducciones experimentales) con dicho funcional.

      Saludos y estoy al pendiente

      • La frecuencia IR es -54.23, lo que quiero observar es la separación entre el O—N del sistema así que digamos que no necesariamente que sea grande pero que sea la frecuencia para este vibración. Y bueno precisamente estoy buscando este estado de transición porque quiero compararlo con lo obtenido experimentalmente. No se si queda claro?

      • Pues si esa frecuencia de -54.23 corresponde a la separación O-N que buscas pues ya terminaste! O estoy entendiendo mal?

  5. Excellent article. Keep writing such kind of information on your blog.
    Im really impressed by it.
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  6. Buenas Joaquin:
    Encontre un TS a nivel HF/3-21G* con una frecuencia imaginaria de -186 cm-1 y el calculo del IRC me da perfecto. Sin embargo al querer reoptimizar esa estructura usando M062X/6-311+G** me genera una estructura con una frecuencia negativa muy pequeña -39 cm-1 y el IRC solo me da dos pasos y se corta. No estoy segura si en realidad es un TS.

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