K. Hemelsoet

TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad variety of advanced models, including the standard full Hessian, the Mobile Block Hessian, the Partial Hessian Vibrational approach, the Vibrational Subsystem Analysis with or without mass matrix correction, the Elastic Network Model, and other combinations. TAMkin is readily extensible because of its modular structure. Chemical kinetics of unimolecular and bimolecular reactions can be analyzed in a straightforward way using conventional transition state theory, including tunneling corrections and internal rotor refinements. A sensitivity analysis can also be performed, providing important insight into the theoretical error margins on the kinetic parameters. Two extensive examples demonstrate the capabilities of TAMkin: the conformational change of the biological system adenylate kinase is studied, as well as the reaction kinetics of the addition of ethene to the ethyl radical. The important feature of batch processing large amounts of data is highlighted by performing an extended level of theory study, which TAMkin can automate significantly.

We present a validation of computationally efficient density functional-based methods for the reproduction of relative bond dissociation energies of large polyaromatic hydrocarbons. Through the calculation of intrinsic radical stabilities and the computation of spin densities, the extent of delocalization of the unpaired electron in the benzylic radicals is examined. We focus on the influence of the level of theory choice applied for the geometry optimization and the role of van der Waals corrections on thermochemical properties. The dispersion effects mainly influence the energetics, causing a small upward shift of the bond dissociation energies. The long-range corrected CAM-B3LYP functional does not improve the traditional B3LYP results for the geometry description of the large delocalized radicals, however a non-negligible influence was encountered when applied for the energetics. It is reported that the f polarization functions present in the 6-311+G(3df,2p) basis set lead to an erroneous trend when combined with the B2PLYP functional for the computation of the single point energies.