# Blog Archives

## The “art” of finding Transition States Part 2

Last week we posted some insights on finding Transitions States in Gaussian 09 in order to evaluate a given reaction mechanism. A stepwise methodology is tried to achieve and this time we’ll wrap the post with two flow charts trying to synthesize the information given. It must be stressed that knowledge about the chemistry of the reaction is of paramount importance since G09 cannot guess the structure connecting two minima on its own but rather needs our help from our chemical intuition. So, without further ado here is the remainder of Guillermo’s post.

**METHOD 3. **QST3. For this method, you provide the coordinates of your reagents, products and TS (in that order) and G09 uses the QST3 method to find the first order saddle point. As for QST2 the numbering scheme must match for all the atoms in your three sets of coordinates, again, use the connection editor to verify it. Here is an example of the input file.

link 0 --blank line-- #p b3lyp/6-31G(d,p)opt=(qst3,calcfc)geom=connectivity freq=noraman --blank line--Charge MultiplicityCoordinates of reagents --blank line—Charge MultiplicityCoordinates of products --blank line--Charge MultiplicityCoordinates of TS --blank line---

As I previously mentioned, it happens that you find a first order saddle point but does not correspond to the TS you want, you find an imaginary vibration that is not the one for the bond you are forming or breaking. For these cases, I suggest you to take that TS structure and manually modify the region that is causing you trouble, then use method 2.

**METHOD 4. **When the previous methods fail to yield your desired TS, the brute force way is to acquire the potential energy surface (PES) and visually locate your possible TS. The task is to perform a rigid PES scan, for this, the molecular structure must be defined using z-matrix. Here is an example of the input file.

link 0 --blank line-- #p b3lyp/6-31G(d,p)scan testgeom=connectivity --blank line--Charge MultiplicityZ-matrix of reagents (or products) --blank line--

In the Z-matrix section you must specify which variables (B, A or D) you want to modify. First, locate the variables you want to modify (distance B, angle A, or dihedral angle D). Then modify those lines within the Z-matrix, here is an example.

B1 1.41 3 0.05 A1 104.5 2 1.0

What you are specifying with this is that the variable B1 (a distance) is going to be stepped 3 times by 0.05. Then variable A1 (an angle) is going to be stepped 2 times by 1.0. Thus, a total of 12 energy evaluations will be performed. At the end of the calculation open the .log file in gaussview and in Results choose the Scan… option. This will open a 3D surface where you should locate the saddle point, this is an educated guess, so take the structure you think corresponds to your TS and use it for method 2.

I have not fully explored this method so I encourage you to go to Gaussian.com and thoroughly review it.

Once you have found your TS structure and via the imaginary vibration confirmed that is the one you are looking for the next step is to verify that your TS connects both your reagents and products in the potential energy surface. For this, an Intrinsic Reaction Coordinate (IRC) calculation must be performed. Here is an example of the input file for the IRC.

link 0 --blank line-- #p b3lyp/6-31G(d,p)irc=calcfcgeom=connectivity --blank line--Charge MultiplicityCoordinates of TS --blank line--

With this input, you ask for an IRC calculation, the default numbers of steps are 20 for each side of your TS in the PES; you must specify the coordinates of your TS or take them from the .chk file of your optimization. In addition, an initial force constant calculation must be made. It often occurs that the calculation fails in the correction step, thus, for complicated cases I hardly suggest to use **irc=calcall**, this will consume very long time (even days) but there is a 95% guaranty. If the number of points is insufficient you can put more within the route section, here is such an example for a complicated case.

link 0 --blank line-- #p b3lyp/6-31G(d,p)irc=(calcall,maxpoints=80)geom=connectivity --blank line--Charge MultiplicityCoordinates of TS --blank line--

With this route section, you are asking to perform an IRC calculation with 80 points on each side of the PES, calculating the force constants at every point. For an even complicated case try adding the **scf=qc** keyword in the route section, quadratic convergence often works better for IRC calculations.

## 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.

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.

QST2)

%chk=file.chk

%nprocshared=n

%mem=nGB

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

Title card for reagents

Q M

Cartesian Coordinates for reagents

—*blank line*—

Title card for products

Q M

Cartesian Coordinates for products

—*blank line*—

QST3)

%chk=file.chk

%nprocshared=n

%mem=nGB

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

Title Card for reagents

Q M

Cartesian Coordinates for reagents

—*blank line*—

Title card for products

Q M

Cartesian Coordinates for products

—*blank lin*e–

Title card for TS

Q M

Cartesian Coordinates for TS

—*blank line*—

**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 eutactic.wordpress.com)

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.

%chk=QST3_2p.chk

%nprocshared=8

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

Title Card

Q M

—*blank line*—

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.