Reaction Parameters

Contributed by Guilherme Menegon Arantes for fDynamo, and pDynamo versions 1.5 and 1.7.2.

Introduction

The specific reaction parameters (SRP) approach develops parameter sets for QC methods that are better adapted for studying particular classes of reaction. Here two sets of SRPs are given that were parametrized for the MNDO family of semiempirical QC methods.

Halide substitutions

PM3 semiempirical parameters were developed to model the nucleophilic reaction shown in the figure where X = {Cl, Br}.

Phosphate reactions

Here you will find specific NDDO semiempirical parameters developed to model phosphate reactions. Parameters for H, C, O, P and S atoms have been specifically calibrated to thiolysis and alcoholysis of phosphate mono and tri-esters, and proton transfers from related thiols, alcohols and phospho-esters. Full information may be found in Arantes and Loos (2006).

Only H, C, O, P and S parameters are distributed. One may try combinations with AM1 or MNDO parameters for other elements, but this is untested and potentially unreliable. Given that several different versions of DYNAMO are in use, parameters in either FORTRAN format (for the fDynamo version) and in both formats used in pDynamo, XPK (for versions < 1.7.2) and YAML (for versions >= 1.7.2), are provided.

For fDynamo, the mopac_parameters.F90 FORTRAN code should be placed in the fDynamo/source directory and the library re-compiled. To use the parameter set, CALL MOPAC_SETUP ( "AM1" ).

For pDynamo, the XPK or YAML files should be included in the appropriate parameters directory (e.g., pdynamo-1.5/pMolecule-1.5/parameters/ or pDynamo-1.7.2/parameters/mndoParameters/). It is unecessary to re-compile. To use the parameter set, call QCModelMNDO ( "mndoModel" = "chops" ), where "chops" is the folder where the parameter files are included. Small differences (up to ~2 kJ/mol) may be found between the published energies and those obtained with pDynamo due to slight differences in numerical constants in the two programs used (geomop and pDynamo).