PyFrag article in J Comp Chem!

"PyFrag – Streamlining your reaction path analysis" is available

in the Journal of Computational Chemistry.

Reference: W.J. van Zeist, C.Fonseca Guerra, F.M. Bickelhaupt; J. Comput. Chem. 29, 312-315, 2008.

Pyfrag Released!

The program PyFrag has been released and is available for download. PyFrag enables user-friendly and routine explorations and analyses of one- or multidimensional potential energy surfaces with the Amsterdam Density Functional (ADF) package. The Python source can be found in the download section. PyFrag is written by Willem-Jan van Zeist and is under development by Lando P. Wolters at the Theoretical Chemistry department at the Vrije Universiteit in Amsterdam. So far it has been mainly used for research in the subgroup of Prof. Dr. F.M. Bickelhaupt.

Why PyFrag?

Recently, the group of Prof. Dr. Bickelhaupt has focused on explaining chemical reactivity by means of the 'Extended Activation Strain' model. PyFrag serves as a valuable tool for this kind of research. Moreover, PyFrag facilitates an easy scan and analysis of any given (possibly multidimensional) potential energy surface. Such a PES can be constructed by PyFrag or can be taking from the output of for example Intrinisc Reaction Coordinate calculations. A short description of the activation strain model and the energy decomposition analysis with ADF is given below.

Extended Activation Strain Model & Energy Decomposition Analysis

Our group has used the Activation Strain model of chemical reactivity to gain insight into various fundamental chemical reactions such as SN(2) reactions and oxidative insertion/reductive elimination. In this model, the activation energy ∆E≠ is decomposed into the activation strain ∆E≠strain and the TS interaction ∆E≠int:

∆E≠= ∆E≠strain + ∆E≠int

The activation strain ∆E≠strain is the strain energy associated with deforming the reactants from their equilibrium geometry to the geometry they acquire in the activated complex. The TS interaction ∆E≠int is the actual interaction energy between the deformed reactants in the transition state. However, a problem is that the position of the TS along the reaction coordinate (ζ = ζTS) has a large effect on the magnitude of ∆E≠strain = ∆E≠strain(ζTS) and ∆E≠int = ∆E≠int(ζTS). It is therefore unsatisfactory to view the decomposition solely at the TS-geometry.

To tackle this problem, we have extended the Activation Strain model from a single-point analysis of the TS to an analysis along the reaction coordinate ζ:

∆E(ζ) = ∆Estrain(ζ) + ∆Eint(ζ)

The energy profile along the reaction coordinate ζ, can be for example computed using the Intrinsic Reaction Coordinate (IRC) method but any potential energy surface can apply. In the case of, for example, a reaction in which a bond is broken, the reaction coordinate can be suitably chosen as the bondlength of that particular bond.
The interaction ∆Eint(ζ) between the strained reactants is further analyzed in the conceptual framework provided by the Kohn-Sham molecular orbital model. Thus, ∆Eint is further decomposed into three physically meaningful terms using a quantitative energy decomposition scheme developed by Ziegler and Rauk.

∆Eint = ∆Velstat + ∆EPauli + ∆Eoi

The term ∆Velstat corresponds to the classical electrostatic interaction between the unperturbed charge distributions of the deformed reactants and is usually attractive. The Pauli repulsion ∆EPauli comprises the destabilizing interactions between occupied orbitals and is responsible for the steric repulsion. The orbital interaction ∆Eoi accounts for charge transfer (interaction between occupied orbitals on one moiety with unoccupied orbitals of the other, including the HOMO–LUMO interactions) and polarization (empty–occupied orbital mixing on one fragment due to the presence of another fragment).

For a list of references, see the Literature section.