How to calculate the Delta G of solvation? This is a question that I get a lot in this blog, so it is about time I wrote a (mini)post on it, and at the same time put an end to this posting drought which has lasted for quite a few months due to a lot of pending work with which I’ve had to catch up. And as usual thanks to everyone who reads, comments, likes, recommends, rates and shares my silly little posts. 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. A successful IRC will link both structures along a single reaction coordinate proving that both reagents and products are linked by the obtained TS. #p m062x/6-31++G(d,p) IRC=(Maxpoints=50,RCFC,phase=(2,1)) Temperature=373.15 SCRF=(Solvent=Water) geom=allcheckįinally, the IRC path can be visualized with GaussView from the Results menu. Initial constant forces are required and these are commonly retrieved from the TS calculation checkpoint file through the RCFC keyword. This calculation will connect the TS structure to those of the products and the reagents. Once we’ve succeeded in finding the structure of our TS we may run an Internal Reaction Coordinate (IRC) calculation. 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 ) 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.Īs I wrote above, there are no guarantees of finding the right TS so many attempts are probably needed. NOTE: It is fundamental that the numbering order is kept constant throughout the molecular specifications of all two, or three, input structures. 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.
In order to find the structures of the transition states we use in Gaussian the Synchronous Transit-guided Quasi-Newton method through the keywords QST2 or QST3. 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. 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 following procedure considers gas phase calculations. 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.