Numerical simulation of the photoisomerization of retinal from the cis to the trans form

摘要

This dissertation describes a tight-binding technique that treats the dynamicsof electrons and ions simultaneously. The main features are a generalized Hellmann-Feynman theorem, a standard, time-dependent, self-consistent-field description andthe interaction picture. The time-dependence is incorporated by using Peierls Substitution.We also apply the velocity-Verlet algorithm to predict the motion of theions.We first test the validity of this semi-empirical tight-binding approach on severalsmaller systems including ethylene, 2-butene, and stilbene. The cis-trans isomerizationis modeled and in each case the results agree well with those obtained fromother computational and empirical methods. Next, we use the tight-binding modelto simulate the photoisomerization of the retinal molecule from its cis to trans form.The results are comparable to those obtained from experiments. The vibrational frequenciesfor retinal obtained using the force-constant techniques in this model agreewell with those obtained from Fourier transform methods and a standard software.The cis-trans isomerization takes 217.91 fs to complete with a field strength of 1.0gauss?cm, which is comparable to 200 fs reported from experiments. The isomerizationdepends on the strength of the vector potential, the time-step of the simulation and also the wavelength of the light. Using different parameters the isomerizationtakes place in 1-2 ps which is within the range reported from experimentation.The present semi-empirical technique provides an excellent compromise betweencomputationally-prohibitive first principles methods and approximate empirical methodsto model the motion of electrons and ions in a large molecule like retinal.