Partial structure factors of a simulated polymer melt

Fully atomistic molecular dynamic simulations were carried out by using the Insight (Insight II 4.0.0 P version) and the Discover-3 programs from MSI with the polymer consortium force field. The model system used in these simulations was built using the Amorphous Cell module. The polymer system simulated was glassy polyisoprene (PI) as used in previous neutron scattering (NS) measurements. A first molecular dynamics at 363 K was run for 1 ns using the Discover-3 program collecting data every 0.01 ps and a subsequent one (taking the previous output sample as an input for the following dynamics) was run for 2 ns collecting data every 0.5 ps. The results of the second run agreed to those of the first run, indicating that the sample was well equilibrated at this high temperature. Starting from the obtained atomic trajectories we have calculated the partial static structure factors for NS corresponding to different PI samples with different levels of deuteration (PId3, i.e., methyl group deuterated and main chain protonated; PId5, i.e., methyl group protonated and main chain deuterated; PId8, i.e., fully deuterated and PIh8, i.e., fully protonated). The results obtained are compared to the coherent NS cross-sections measured on real samples by means of D7 spectrometer with polarization analysis (ILL, Grenoble). A good agreement is obtained between experimental and simulated data validating the simulated sample. Moreover, the dynamic evolution of these correlations has also been calculated from the simulations. With these time dependent functions, the magnitude measured in a neutron spin echo (NSE) experiment can be constructed. Here we present two examples dealing with the fully deuterated sample PId8 and a partially deuterated sample, PId5, that show how computer simulation constitutes an invaluable tool for interpreting NSE results.