Semiquantitative model for response of biological molecules containing C, N, O and H to laser pulses, with initial application to dipicolinic acid

We have constructed a semiquantitative model which can be used to treat the response of molecules containing carbon, nitrogen, oxygen and hydrogen to ultrafast laser pulses. The parameters for the pairwise interaction of both nitrogen and oxygen are obtained from a simple scaling of carbon and hydrogen parameters calculated by Frauenheim and co-workers. For the initial application of this model, we have chosen dipicolinic acid (DPA), an important constituent of biological spores. The equilibrium bond lengths of all of the test molecules, including DPA, are within 5% of the experimental bond lengths. The calculated molecular orbital structure of DPA near the HOMO–LUMO gap region shows three nearly degenerate occupied molecular orbitals and two nearly degenerate unoccupied orbitals. Photoexcitation with an ultrashort 5 fs FWHM laser pulse matched to the HOMO–LUMO gap energy produced transitions from the lowest of the the three nearly degenerate occupied orbitals to both of the nearly degenerate unoccupied molecular orbitals. The precise nature of the transition depends on the polarization of the laser pulse. These results are shown to be in qualitative agreement with fully ab initio methods.